Skip to main content
SpringerLink
Log in

Bacteria of the Genus Sphaerochaeta from Low-Temperature Heavy Oil Reservoirs (Russia)

  • EXPERIMENTAL ARTICLES
  • Published:
Microbiology Aims and scope Submit manuscript

Abstract—

Fermenting bacteria are usual components of oilfield microbial communities. Since pure cultures of fermenting bacteria utilize carbohydrates and do not grow on oil, their diversity and relationships in the community are of great interest. In the present work, enrichment and pure cultures of fermenting bacteria obtained from formation water of low-temperature oilfields (Russia) were studied. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene was carried out for an enrichment culture. The library was found to contain the genes of anaerobic bacteria of the genus Halanaerobium, which are capable of growth on polysaccharides with thiosulfate reduction to sulfide, as well as the genes of Abyssivirga alkaniphila, which grows on C5–C25n-alkanes of oil with thiosulfate as an electron acceptor or in a syntrophic association with hydrogenotrophic methanogens. Members of the genus Sphaerochaeta were minor components of the community. Three strains (4-11, 5-8-5, and 17-50) were isolated from enrichment cultures. The isolates were anaerobic mesophilic slightly halophilic bacteria, which fermented a number of carbohydrates and grew as biofilms. The 16S rRNA gene sequences of the new strains exhibited 99.5–100% similarity between each other and 97.2–98.0% similarity to the sequences of the most closely related species Sphaerochaetaassociata and Sphaerochaetaglobosa, which indicated their affiliation to a new Sphaerochaeta species. The products of maltose fermentation were acetate, propionate, СО2, Н2, and sometimes iso-propanol. The strains did not grow on crude oil. In oilfields Sphaerochaeta species probably consume the products of oil biodegradation by other microorganisms, are involved in biofilms formation, and provide H2 for methanogens and other components of the community.

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.
Fig. 2.

Similar content being viewed by others

REFERENCES

  1. Abt, B., Han, C., Scheuner, C., Lu, M., Lapidus, A., Nolan, M., Lucas, S., Hammon, N., Deshpande, S., Cheng, J.-F., Tapia, R., Goodwin, L., Pitluck, S., Mavromatis, K., Mikhailova, N. et al., Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta, Stand. Genom. Sci., 2012, vol. 6, pp. 194–209.

    Article  CAS  Google Scholar 

  2. Arroua, B., Ranchou-Peyruse, A., Ranchou-Peyruse, M., Magot, M., Urios, L., and Grimaud, R., Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta, Int. J. Syst. Evol. Microbiol., 2017, vol. 67, pp. 417–424.

    Article  CAS  PubMed  Google Scholar 

  3. Bolger, A.M., Lohse, M., and Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 2014, vol. 30, pp. 2114–2120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bonch-Osmolovskaya, E.A., Miroshnichenko, M.L., Lebedinsky, A.V., Chernyh, N.A., Nazina, T.N., Ivoilov, V.S., Belyaev, S.S., Boulygina, E.S., Lysov, Yu.P., Perov, A.N., Mirzabekov, A.D., Hippe, H., Stackebrandt, E., L’Haridon, S., and Jeanthon, C., Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir, Appl. Environ. Microbiol., 2003, vol. 69, pp. 6143–6151.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E. et al., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 2010, vol. 7, pp. 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Dahle, H., Garshol, F., Madsen, M., and Birkeland, N., Microbial community structure analysis of produced water from a high-temperature North Sea oil-field, Antonie van Leeuwenhoek, 2008, vol. 93, pp. 37–49.

    Article  PubMed  Google Scholar 

  7. Dröge, S, Fröhlich, J, Radek, R, and König, H., Spirochaeta coccoides sp. nov., a novel coccoid spirochete from the hindgut of the termite Neotermes castaneus, Appl. Environ. Microbiol., 2006, vol. 72, pp. 392–397.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Fadrosh, D.W., Ma, B., Gajer, P., Sengamalay, N., Ott, S., Brotman, R.M., and Ravel, J., An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform, Microbiome, 2014, vol. 2, p. 6.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Folarin, Y., An, D., Caffrey, S., Soh, J., Sensen, C.W., Voordouw, J., Jack, T., and Voordouw, G., Contribution of make-up water to the microbial community in an oilfield from which oil is produced by produced water re-injection, Int. Biodeterior. Biodegrad., 2013, vol. 81, pp. 44–50.

    Article  CAS  Google Scholar 

  10. Gao, P., Tian, H., Li, G., Sun, H., and Ma, T., Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir, Microbiology Open, 2015, vol. 4, pp. 332–342.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Grabowski, A., Nercessian, O., Fayolle, F., Blanchet, D., and Jeanthon, C., Microbial diversity in production waters of a low-temperature biodegraded oil reservoir, FEMS Microbiol. Ecol., 2005, vol. 54, pp. 427–443.

    Article  CAS  PubMed  Google Scholar 

  12. Gray, N.D., Sherry, A., Hubert, C., Dolfing, J., and Head, I.M., Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery, Adv. Appl. Microbiol., 2010, vol. 72, pp. 137–161.

    Article  CAS  PubMed  Google Scholar 

  13. Kevbrin, V.V. and Zavarzin, G.A., Effect of sulfur compounds on growth of a halophilic homoacetogenic bacterium Acetohalobium arabaticum, Mikrobiologiya, 1992, vol. 61, pp. 812–817.

    CAS  Google Scholar 

  14. Lane, D.J., 16S/23S rRNA sequencing, in Nucleic Acid Techniques in Bacterial Systematics, Stackebrandt, E. and Goodfellow, M., Eds., New York: Wiley, 1991, pp. 115–175.

    Google Scholar 

  15. Liang, R., Davidova, I.A., Marks, C.R., Stamps, B.W., Harriman, B.H., Stevenson, B.S., Duncan, K.E., and Suflita, J.M., Metabolic capability of a predominant Halanaerobium sp. in hydraulically fractured gas wells and its implication in pipeline corrosion, Front. Microbiol., 2016, vol. 7, p. 988. doi 10.3389/fmicb.2016.00988

  16. Magot, M., Fardeau, M.-L., Arnauld, O., Lanau, C., Ollivier, B., Thomas, P., and Patel, B.K.C., Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field, FEMS Microbiol. Lett., 1997, vol. 155, pp. 185–191.

    Article  CAS  PubMed  Google Scholar 

  17. Maniatis, T., Fritsh, E.F., Sambrook, J., and Engel, J., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Laboratory Press, 1982.

    Google Scholar 

  18. Nazina, T.N., Shestakova, N.M., Semenova, E.M., Korshunova, A.V., Kostrukova, N.K., Tourova, T.P., Min, L., Feng, Q., and Poltaraus, A.B., Diversity of metabolically active Bacteria in water-flooded high-temperature heavy oil reservoir, Front. Microbiol., 2017, vol. 8, p. 707. doi 10.3389/fmicb.2017.00707

  19. Nazina, T.N., Sokolova, D.Sh., Babich, T.L., Semenova, E.M., Ershov, A.P., Bidzhieva, S.Kh., Borzenkov, I.A., Poltaraus, A.B., Khisametdinov, M.R., and Tourova, T.P., Microorganisms of low-temperature heavy oil reservoirs (Russia) and their possible application for enhanced oil recovery, Microbiology (Moscow), 2017, vol. 86, pp. 773–785.

    Article  CAS  Google Scholar 

  20. Pham, V.D., Hnatow, L.L., Zhang, S., Fallon, R.D., Jackson, S.C., Tomb, J.F., DeLong, E.F., and Keeler, S.J., Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods, Environ. Microbiol., 2009, vol. 11, pp. 176–187.

    Article  CAS  PubMed  Google Scholar 

  21. Postgate, J.R., The Sulfate-Reducing Bacteria, 2nd ed., Cambridge: Cambridge Univ. Press, 1984.

    Google Scholar 

  22. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F.O., The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucl. Acids Res., 2013, vol. 41, no. D1, pp. D590‒D596.

    Article  CAS  PubMed  Google Scholar 

  23. Ritalahti, K.M., Justicia-Leon, S.D., Cusick, K.D., Ramos-Hernandez, N., Rubin, M., Dornbush, J., and Loffler, F.E., Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes, Int. J. Syst. Evol. Microbiol., 2012, vol. 62, pp. 210–216.

    Article  CAS  PubMed  Google Scholar 

  24. Schouw, A., Eide, T.L., Stokke, R., Pedersen, R.B., Steen, I.H., and Bodtker, G., Abyssivirga alkaniphila, gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica, Int. J. Syst. Evol. Microbiol., 2016, vol. 66, pp. 1724–1734.

    Article  CAS  PubMed  Google Scholar 

  25. Shivani, Y., Subhash, Y., Sasikala, C., and Ramana, C.V., Description of “Candidatus Marispirochaeta associata” and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica com. nov., Int. J. Syst. Evol. Microbiol., 2016, vol. 66, pp. 5485–5492.

    Article  CAS  PubMed  Google Scholar 

  26. Silva, T.R., Verde, L.C.L., Santos Neto, E.V., and Oliveira, V.M., Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields, Int. Biodeterior. Biodegrad., 2013, vol. 81, pp. 57–70.

    Article  CAS  Google Scholar 

  27. Takahashi, S., Tomita, J., Nishioka, K., Hisada, T., and Nishijima, M., Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing, PLoS One, 2014, vol. 9, no. 8, e105592.

    Article  CAS  Google Scholar 

  28. Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions specific gap penalties and weight matrix choice, Nucl. Acids Res., 1994, vol. 9, pp. 3251–3270.

    Google Scholar 

  29. Troshina, O., Oshurkova, V., Suzina, N., Machulin, A., Ariskina, E., Vinokurova, N., Kopitsyn, D., Novikov, A., and Shcherbakova, V., Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01, Int. J. Syst. Evol. Microbiol., 2015, vol. 65, pp. 4315–4322.

    Article  CAS  PubMed  Google Scholar 

  30. Van de Peer, Y. and De Wachter, R., TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment, Comput. Appl. Biosci., 1994, vol. 10, pp. 569–570.

    CAS  PubMed  Google Scholar 

  31. Van der Kraan, G.M., Bruining, J., Lomans, B.P., van Loosdrecht, M.C.M., and Muyzer, G., Microbial diversity of an oil-water processing site and its associated oil field: the possible role of microorganisms as information carriers from oil-associated environments, FEMS Microbiol. Ecol., 2010, vol. 71, pp. 428–443.

    Article  CAS  PubMed  Google Scholar 

  32. Wang, L.Y., Ke, W.J., Sun, X.B., Liu, J.F., Gu, J.D., and Mu, B.Z., Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches, Appl. Microbiol. Biotechnol., 2014, vol. 98, pp. 4209–4221.

    Article  CAS  PubMed  Google Scholar 

  33. Wolin, E.A., Wolin, M.J., and Wolfe, R.S., Formation of methane by bacterial extracts, J. Biol. Chem., 1963, vol. 238, pp. 2882–2888.

    CAS  PubMed  Google Scholar 

  34. Zeikus, G., Hegge, P.W., Thompson, T.E., Phelps, T.J., and Langworthy, T.A., Isolation and description of Haloanaerobium praevalens gen. nov. and sp. nov., an obligately anaerobic halophile common to Great Salt Lake sediments, Curr. Microbiol., 1983, vol. 9, pp. 225–234.

    Article  CAS  Google Scholar 

  35. Zhang, F., She, Y.-H., Chai, L.-J., Banat, I.M., Zhang, X.-T., Shu, F.-C., Wang, Z.-L., Yu, L.-J., and Hou, D.-J., Microbial diversity in long-term water-flooded oil reservoirs with different in situ temperatures in China, Sci. Rep., 2012, vol. 2. article 760. doi 10.1038/srep00760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

ACKNOWLEDGMENTS

The authors are grateful to A.Yu. Merkel (Research Center of Biotechnology, Russian Academy of Sciences) for carrying out high-throughput sequencing of the 16S rRNA genes from the fermenting enrichment. The work was supported by the Russian Science Foundation, project no. 16-14-00028.

Author information

Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia

    S. Kh. Bidzhieva, D. Sh. Sokolova, T. P. Tourova & T. N. Nazina

Authors
  1. S. Kh. Bidzhieva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. Sh. Sokolova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. P. Tourova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. T. N. Nazina
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T. N. Nazina.

Additional information

Translated by P. Sigalevich

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bidzhieva, S.K., Sokolova, D.S., Tourova, T.P. et al. Bacteria of the Genus Sphaerochaeta from Low-Temperature Heavy Oil Reservoirs (Russia). Microbiology 87, 757–765 (2018). https://doi.org/10.1134/S0026261718060048

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026261718060048

Keywords:

Search

Navigation