Some characteristics of the microbial community of reservoir fluids of the Romashkinskoe field
Institutes and Faculties
Main page \ Research and Innovations \ Publications \ Publishing activities of KFU \ Uchenye Zapiski Kazanskogo Universiteta \ Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki \ Archive

Some characteristics of the microbial community of reservoir fluids of the Romashkinskoe field

L.R. Biktasheva*, S.Y. Selivanovskaya**, R.A. Mukhtarova***, H. Abdaljialil****, P.Y. Galitskaya*****

Kazan Federal University, Kazan, 420008 Russia

E-mail: *biktasheval@mail.ru, **svetlana.selivanovskaya@kpfu.ru, ***rene.2020@yandex.ru, ****hasanabdaljialil23@gmail.com, *****gpolina33@yandex.ru

Received December 23, 2021

ORIGINAL ARTICLE

Full text PDF

DOI: 10.26907/2542-064X.2022.2.263-278

For citation: Biktasheva L.R., Selivanovskaya S.Y., Mukhtarova R.A., Abdaljialil H., Galit­skaya P.Y. Some characteristics of the microbial community of reservoir fluids of the Romashkinskoe field. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2022, vol. 164, no. 2, pp. 263–278. doi: 10.26907/2542-064X.2022.2.263-278. (In Russian)

Abstract

The condition of oil wells is reflected by the abundance and species composition of microorganisms in their reservoir fluids. However, such microorganisms are often present in small numbers, which hampers their analysis. The culture enrichment method is a good strategy to overcome this problem. Here we discuss the results of a molecular biology-based comparative analysis of some characteristics of the microbial communities from the following two samples: the initial reservoir fluid sample (2313A) and the enriched sample (2313B).

The metagenomic analysis showed that sample 2313A was dominated by aerobic bacteria belonging to the genera Pseudomonas (order Pseudomonales) (47.5%) and Rhodococcus (order Actinomycetales) (45%). The community also comprised representatives of the anaerobic orders Halanaerobiales (1.4%) and Desulfovibrionales (0.03%). In sample 2313B, bacteria from the phylum Actinobacteria prevailed (99.9%) with Rhodococcus fascians (order Actinomycetales) identified as the dominant OTU. The quantitative real-time PCR analysis revealed that the enrichment process led to a 1063 and 244 times decrease in the relative abundance of copies of the rhlB and rhlAB genes encoding enzymes for the production of biosurfactants. The cultivation had a lesser effect on the abundance of copies of the dsrA and apsA genes, both involved in the sulfate reduction. When summarized, the obtained results indicate that the culture enrichment method enables the formation of a community differing substantially from the initial microbial communities of reservoir fluids of the oil wells.

Keywords: reservoir fluid, bacterial community, sulfate reduction, biosurfactants

Acknowledgments. This study was supported by the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2020-931) within the framework of the development program of a world-class research center “Efficient development of the global liquid hydrocarbon reserves”.

Figure Captions

Fig. 1. Community structure of samples 2313A and 2313B with OTU grouping at the phylum level (similarity threshold of 97%).

Fig. 2. Community structure of samples 2313A and 2313B with the OTU grouping at the level of orders and genera (similarity threshold of 97%).

Fig. 3. Number of copies of 16S rRNA genes determined for samples 2313A and 2313B.

Fig. 4. Relative number of copies of genes encoding the synthesis of biosurfactants: a – rhlA, b – rhlAB, c – rhlB, d – rhlR.

Fig. 5. Relative number of copies of genes encoding sulfate reduction enzymes (dsrA, apsA).

References

  1. Vigneron A., Alsop E.B., Lomans B.P., Kyrpides N.C., Head I.M., Tsesmetzis N. Succession in the pet­roleum reservoir microbiome through an oil field production lifecycle. ISME J., 2017, vol. 11, no. 9, pp. 2141–2154. doi: 10.1038/ismej.2017.78.
  2. Sierra-Garcia I.N., Belgini D.R.B., Torres-Ballesteros A., Paez-Espino D., Capilla R., Santos Neto E.V., Gray N., de Oliveira V.M. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. Sci. Total Environ., 2020, vol. 715, art. 136646, pp. 1–14. doi: 10.1016/j.scitotenv.2020.136646.
  3. Korenblum E., Souza D.B., Penna M., Seldin L. Molecular analysis of the bacterial communities in crude oil samples from two Brazilian offshore petroleum platforms. Int. J. Microbiol., 2012, vol. 2012, art. 156537, pp. 1–8. doi: 10.1155/2012/156537.
  4. Pannekens M., Kroll L., Müller H., Mbow F.T., Meckenstock R.U. Oil reservoirs, an exceptional habitat for microorganisms. New Biotechnol., 2019, vol. 49, pp. 1–9. doi: 10.1016/j.nbt.2018.11.006.
  5. Wang M., Deng B., Fu X., Sun H., Xu Z. Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil. Environ. Pollut., 2019, vol. 255, pt. 1, art. 113190, pp. 1–10. doi: 10.1016/j.envpol.2019.113190.
  6. Li J., Feng M., Yu X. Rapid detection of mcyG gene of microcystins producing  cyanobacteria in water samples by recombinase polymerase amplification combined with lateral flow strips. J. Water Health, 2021, vol. 19, no. 6, pp. 907–917. doi: 10.2166/wh.2021.091.
  7. Blazejak A., Schippers A. Real-time PCR quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing prokaryotes in marine sediments of the Peru continental margin and the Black Sea. Front. Microbiol., 2011, vol. 2, art. 253, pp. 1–11. doi: 10.3389/fmicb.2011.00253.
  8. Gittel A., Sørensen K.B., Skovhus T.L., Ingvorsen K., Schramm A. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl. Environ. Microbiol., 2009, vol. 75, no. 22, pp. 7086–7096. doi: 10.1128/AEM.01123-09.
  9. Fritz G., Büchert T., Huber H., Stetter K.O., Kroneck P.M.H. Adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes – high similarity of molecular properties emphasizes their central role in sulfur metabolism. FEBS Lett., 2000, vol. 473, no. 1, pp. 63–66. doi: 10.1016/s0014-5793(00)01500-3.
  10. Klein M., Friedrich M., Roger A.J., Hugenholtz P., Fishbain S., Abicht H., Blackall L.L., Stahl D.A., Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol., 2001, vol. 183, no. 20, pp. 6028–6035. doi: 10.1128/JB.183.20.6028-6035.2001.
  11. Wagner M., Roger A.J., Flax J.L., Brusseau G.A., Stahl D.A. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol., 1998, vol. 180, no. 11, pp. 2975–2982. doi: 10.1128/JB.180.11.2975-2982.1998.
  12. Zverlov V., Klein M., Lücker S., Friedrich M.W., Kellermann J., Stahl D.A., Loy A., Wagner M. Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. J. Bacteriol., 2005, vol. 187, no. 6, pp. 2203–2208. doi: 10.1128/JB.187.6.2203-2208.2005.
  13. Dulcey C.E., López de los Santos Y., Létourneau M., Déziel E., Doucet N. Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. FEBS J., 2019, vol. 286, no. 20, pp. 4036–4059. doi: 10.1111/febs.14954.
  14. Twigg M.S., Tripathi L., Zompra A., Salek K., Irorere V.U., Gutierrez T., Spyroulias G.A., Marchant R., Banat I.M. Identification and characterisation of short chain rhamnolipid production in a previously uninvestigated, non-pathogenic marine pseudomonad. Appl. Microbiol. Biotechnol., 2018, vol. 102, no. 19, pp. 8537–8549. doi: 10.1007/s00253-018-9202-3.
  15. Ferrari B.C., Binnerup S.J., Gillings M. Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria. Appl. Environ. Microbiol., 2005, vol. 71, no. 12, pp. 8714–8720. doi: 10.1128/AEM.71.12.8714-8720.2005.
  16. Dellagnezze B.M., Vasconcellos S.P., Angelim A.L., Melo V.M.M., Santisi S., Cappello S., Oliveira V.M. Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale. Mar. Pollut. Bull., 2016, vol. 107, no. 1, pp. 107–117. doi: 10.1016/j.marpolbul.2016.04.011.
  17. von der Weid I., Korenblum E., Jurelevicius D., Rosado A.S., Dino R., Sebastian G.V., Seldin L. Molecular diversity of bacterial communities from subseafloor rock samples in a deep-water production basin in Brazil. J. Microbiol. Biotechnol., 2008, vol. 18, no. 1, pp. 5–14.
  18. Voget S., Leggewie C., Uesbeck A., Raasch C., Jaeger K.-E., Streit W.R. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol., 2003, vol. 69, no. 10, pp. 6235–6242. doi: 10.1128/AEM.69.10.6235-6242.2003.
  19. Muyzer G., de Waal E., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain. Appl. Environ. Microbiol., 1993, vol. 59, no. 3, pp. 695–700. doi: 10.1128/aem.59.3.695-700.1993.
  20. Shahsavari E., Aburto-Medina A., Taha M., Ball A.S. A quantitative PCR approach for quantification of functional genes involved in the degradation of polycyclic aromatic hydrocarbons in contaminated soils. MethodsX, 2016, vol. 3, pp. 205–211. doi: 10.1016/j.mex.2016.02.005.
  21. Xu K., Tang Y., Ren C., Zhao K., Sun Y. Diversity and abundance of n-alkane-degrading bacteria in the near-surface soils of a Chinese onshore oil and gas field. Biogeosciences, 2013, vol. 10, pp. 2041–2048. doi: 10.5194/bg-10-2041-2013.
  22. Fukuhara Y., Horii S., Matsuno T., Matsumiya Y., Mukai M., Kubo M. Distribution of hydrocarbon-degrading bacteria in the soil environment and their contribution to bioremediation. Appl. Biochem. Biotechnol., 2013, vol. 170, no. 2, pp. 329–339. doi: 10.1007/s12010-013-0170-x.
  23. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by      denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes       coding for 16S rRNA. Appl. Environ. Microbiol., 1993, vol. 59, no. 3, pp. 695–700. doi: 10.1128/aem.59.3.695-700.1993.
  24. Ben-Dov E., Brenner A., Kushmaro A. Quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (PCR) Using dsrA and apsA genes. Microb. Ecol., 2007, vol. 54, no. 3, pp. 439–451. doi: 10.1007/s00248-007-9233-2.
  25. Karunakaran E., Vernon D., Biggs C.A., Saul A., Crawford D., Jensen H. Enumeration of sulphate-reducing bacteria for assessing potential for hydrogen sulphide production in urban drainage systems. Water Sci. Technol., 2016, vol. 73, no. 12, pp. 3087–3094. doi: 10.2166/wst.2016.026.
  26. Bodour A.A., Drees K.P., Maier R.M. Distribution of biosurfactant-producing bacteria in undisturbed and contaminated arid southwestern soils. Appl. Environ. Microbiol., 2003, vol. 69, no. 6, pp. 3280–3287. doi: 10.1128/AEM.69.6.3280-3287.2003.
  27. Medina G., Juárez K., Valderrama B., Soberón-Chávez G. Mechanism of Pseudomonas aeruginosa RhlR transcriptional regulation of the rhlAB promoter. J. Bacteriol., 2003, vol. 185, no. 20, pp. 5976–5983. doi: 10.1128/JB.185.20.5976-5983.2003.
  28. Medina G., Juárez K., Díaz R., Soberón-Chávez G. Transcriptional regulation of Pseudomonas aeruginosa rhlR, encoding a quorum-sensing regulatory protein. Microbiology, 2003, vol. 149, no. 11, pp. 3073–3081. doi: 10.1099/mic.0.26282-0.
  29. Agrawal A., Lal B. Rapid detection and quantification of bisulfite reductase genes in oil field samples using real-time PCR. FEMS Microbiol. Ecol., 2009, vol. 69, no. 2, pp. 301–312. doi: 10.1111/j.1574-6941.2009.00714.x.
  30. Wang L.-Y., Ke W.-J., Sun X.-B., Liu J.-F., Gu J.-D., 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, no. 9, pp. 4209–4221. doi: 10.1007/s00253-013-5472-y.
  31. Maes T., Vereecke D., Ritsema T., Cornelis K., Thu H.N.T., Van Montagu M., Holsters M., Goethals K. The att locus of Rhodococcus fascians strain D188 is essential for full virulence on tobacco through the production of an autoregulatory compound. Mol. Microbiol., 2001, vol. 42, no. 1, pp. 13–28. doi: 10.1046/j.1365-2958.2001.02615.x.
  32. Muscatello G., Anderson G.A., Gilkerson J.R., Browning G.F. Associations  between  the ecology of virulent Rhodococcus equi and the epidemiology of R. equi pneumonia on Australian  tho­roughbred farms. Appl. Environ. Microbiol., 2006, vol. 72, no. 9, pp. 6152–6160. doi: 10.1128/AEM.00495-06.
  33. Fanget N.V.J., Foley S. Starvation/stationary-phase survival of Rhodococcus erythropolis SQ1: A physiological and genetic analysis. Arch. Microbiol., 2011, vol. 193, no. 1, pp. 1–13. doi: 10.1007/s00203-010-0638-9.

The content is available under the license Creative Commons Attribution 4.0 License.

Вход в личный кабинет
Ваш логин
Ваш пароль
Забыли пароль? Регистрация