Degradation of diesel fuel by <em>Dietzia</em> sp. Ndt10 in saline conditions

Alexey Nazarov; Anna Pyankova; Ekaterina Korsakova; Elena Plotnikova

doi:10.21638/spbu03.2024.201

Authors

Alexey Nazarov All-Russia Research Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, ul. Goleva, 13, Perm, 614081, Russian Federation https://orcid.org/0000-0003-4753-4061
Anna Pyankova All-Russia Research Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, ul. Goleva, 13, Perm, 614081, Russian Federation https://orcid.org/0000-0003-2210-783X
Ekaterina Korsakova All-Russia Research Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, ul. Goleva, 13, Perm, 614081, Russian Federation https://orcid.org/0000-0002-6907-7562
Elena Plotnikova All-Russia Research Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, ul. Goleva, 13, Perm, 614081, Russian Federation https://orcid.org/0000-0002-0107-0719

DOI:

https://doi.org/10.21638/spbu03.2024.201

Abstract

This study investigated the degradation of diesel fuel (DF) by an aerobic halotolerant strain, Dietzia sp. NDT10 (VKM Ac-2994D), under high salinity conditions. Dietzia sp. strain NDT10 has been isolated from diesel-contaminated rhizosphere soil of Dactylis glomerata L. on the territory of industrial production and processing of potassium salts (Solikamsk, Perm Krai, Russia). The 16S rRNA gene sequence analysis showed that the strain NDT10 is phylogenetically close (99.89 % similarity) to the type strains of two species, Dietzia maris DSM 43672^T and Dietzia kunjamensis subsp. The ability of the strain NDT10 to degrade diesel fuel without salt and in the presence of up to 125 g NaCl/L was found. When adding 30, 50, and 70 g NaCl/L to the culture medium, the diesel fuel degradation ability of strain NDT10 was markedly increased, especially in the case of long-chain hydrocarbons (С₁₅–С₂₀) compared with short-chain hydrocarbons (С₉–С₁₄). An improvement in the degradative activity of Dietzia sp. NDT10 correlated with an increase in cell surface hydrophobicity in the presence of NaCl in the medium. Using the NDT10 strain as an example, a positive effect of diesel fuel components on the salt tolerance of bacteria was established. The results obtained can be used to develop biotechnological strategies for the clean-up of contaminated sites with DF and other petroleum products.

Keywords:

diesel fuel, Dietzia, biodegradation, cell surface hydrophobicity, halotolerance

Downloads

Download data is not yet available.

References

Abatenh, E., Gizaw, B., Tsegaye, Z., and Wassie, M. 2017. Application of microorganisms in bioremediation-review. Journal of Environmental Microbiology 1(1):2–9. https://doi.org/10.17352/ojeb.000007

Abed, R. M. M., Al-Kharusi, S., and Al-Hinai, M. 2015. Effect of biostimulation, temperature and salinity on respiration activities and bacterial community composition in an oil polluted desert soil. International Biodeterioration and Biodegradation 98:43–52. https://doi.org/10.1016/j.ibiod.2014.11.018

Auffret, M., Labbe, D., Thouand, G., Greer, C. W., and Fayolle-Guichard, F. 2009. Degradation of a mixture of hydrocarbons, gasoline, and diesel oil addi-tives by Rhodococcus aetherivorans and Rhodococcus wratislaviensis. Applied and Environmental Microbiology 75(24):7774–7782. https://doi.org/10.1128/AEM.01117-09

Banciu, H. L. and Sorokin, D. Y. 2013. Adaptation in haloalkaliphiles and natronophilic bacteria; pp. 121–178 in Seckbach, J., Oren, A., and Stan-Lotter, H. (eds), Polyextremophiles: life under multiple forms of stress (cellular origin, life in extreme habitats and astrobiology). Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6488-0_5

Bastiaens, L., Springael, D., Wattiau, P., Harms, H., de Wachter, R., Verachtert, H., and Diels, L. 2000. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Applied and Environmental Microbiology 66(5):1834–1843. https://doi.org/10.1128/AEM.66.5.1834-1843.2000

Bødtker, G, Hvidsten, I. V., and Torsvik, B. T. 2009. Hydrocarbon degradation by Dietzia sp. A14101 isolated from an oil reservoir model column. Antonie Van Leeuwenhoek 96:459–469. https://doi.org/10.1007/s10482-009-9359-y

Bos, R., van der Mei, H. C., and Busscher, H. J. 1999. Physico-chemistry of initial microbial adhesive interactions–its mechanisms and methods for study. FEMS Microbiology Reviews 23(2):179–230. https://doi.org/10.1111/j.1574-6976.1999.tb00396.x

Bredholt, H., Bruheim, P., Potocky, M., and Eimhjellen, K. 2002. Hydrophobicity development, alkane oxidation, and crude-oil emulsification in a Rhodococcus species. Canadian Journal of Microbiology 48(2):295–304. https://doi.org/10.1139/w02-024

Brzeszcz, J. and Kaszycki, P. 2018. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diver-sity and flexibility. Biodegradation 29(4):359–407. https://doi.org/10.1007/s10532-018-9837-x

Cao, Y., Zhang, B., Zhu, Z., Song, X., Cai, Q., Chen, B., and Ye, X. 2020. Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation. Science of the Total Environment 727:138723. https://doi.org/10.1016/j.scitotenv.2020.138723

Chen, W., Li, J., Xun, S., Min, J., and Hu, X. 2017. High efficiency degradation of alkanes and crude oil by a salt-tolerant bacterium Dietzia species CN-3. International Biodeterioration and Biodegradation 118:110-118. https://doi.org/10.1016/j.ibiod.2017.01.029

Chandra, S., Sharma, R., Singh, K., and Sharma, A. 2013. Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon. Annals of Microbiology 63:417–431. https://doi.org/10.1007/s13213-012-0543-3

Chang, W., Akbari, A., David, C. A., and Ghoshal, S. 2018. Selective biostimulation of cold- and salt-tolerant hydrocarbon-degrading Dietzia maris in petroleum-contaminated sub-Arctic soils with high salinity. Chemical Technology and Biotechnology 93(1):294–304. https://doi.org/10.1002/jctb.5385

de Carvalho, C. C. C. R. 2012. Adaptation of Rhodococcus erythropolis cells for growth and bioremediation under extreme conditions. Research in Microbiology 163(2):125–136. https://doi.org/10.1016/j.resmic.2011.11.003

de Carvalho, C. C. C. R., Fatal, V., Alves, S. S., and da Fonseca, M. M. R. 2007. Adaptation of Rhodococcus erythropolis cells to high concentrations of toluene. Applied Microbiology and Biotechnology 76:1423–1430. https://doi.org/10.1007/s00253-007-1103-9

de Carvalho, C. C. C. R., Marques, M. P. C., Hachicho, N., and Heipieper, H. J. 2014. Rapid adaptation of Rhodococcus erythropolis cells to salt stress by synthesizing polyunsaturated fatty acids. Applied Microbiology and Biotechnology 98:5599–5606. https://doi.org/10.1007/s00253-014-5549-2

Edbeib, M. F., Wahab, R. A., and Huyop, F. 2016. Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World Journal of Microbiology and Biotechnology 32(8):135. https://doi.org/10.1007/s11274-016-2081-9

Gharibzahedi, S. M. T., Razavi, S. H., and Mousavi, S. M. 2014. Characterization of bacteria of the genus Dietzia: an updated review. Annals of Microbiology 64:1–11. https://doi.org/10.1007/s13213-013-0603-3

Gori, K., Mortensen, H. D., Arneborg, N., and Jespersen, L. 2005. Expression of the GPD1 and GPP2 orthologues and glycerol retention during growth of Debaryomyces hansenii at high NaCl concentrations. Yeast 22(15):1213–1222. https://doi.org/10.1002/yea.1306

Hart, D. J. and Vreeland, R. H. 1988. Changes in the hydrophobic-hydrophilic cell surface character of Halomonas elongate in response to NaCl. Journal of Bacteriology 170(1):132–135. https://doi.org/10.1128/jb.170.1.132-135.1988

Hu, X., Li, D., Qiao, Y., Song, Q., Guan, Z., Qiu, K., Cao, J., and Huang, L. 2020. Salt tolerance mechanism of a hydrocarbon-degrading strain: salt tolerance mediated by accumulated betaine in cells. Journal of Hazardous Materials 392:122326. https://doi.org/10.1016/j.jhazmat.2020.122326

Hvidsten, I., Mjøs, S. A., Bødtker, G., and Barth, T. 2015. Fatty acids in bacterium Dietzia sp: grown on simple and complex hydrocarbons determined as FAME by GC-MS. Chemistry and Physics of Lipids 190:15–26. https://doi.org/10.1016/j.chemphyslip.2015.06.002

Ivanova, A. E., Sukhacheva, M. V., Kanat’eva, A. Yu., Kravchenko, I. K., and Kurganov, A. A. 2014. Hydrocarbon-oxidizing potential and the genes for n-alkane biodegradation in a new acidophilic microbial association from sulfur blocks. Microbiology (Moscow) 83(6):764–772. https://doi.org/10.1134/S0026261714060095

Kushner, D. J. 1978. Life in high salt and solute concentrations: Halophilic bacteria; pp. 317–368 in Kushner, D. J. (ed.), Microbial Life in Extreme Environments. Academic Press, London.

Khalid, F. E., Lim, Z. S., Sabri, S., Gomez-Fuentes, C., Zulkharnain, A., and Ahmad, S. A. 2021. Bioremediation of diesel contaminated marine water by bacteria: a review and bibliometric analysis. Journal of Marine Science and Engineering 9(2):155. https://doi.org/10.3390/jmse9020155

Kogej, T., Stein, M., Volkmann, M., Gorbushina, A. A., Galinski, E. A., and Gunde-Cimerman, N. 2007. Osmotic adaptation of the halophilic fungus Hortaea werneckii: role of osmolytes and melanization. Microbiology 153:4261–4273. https://doi.org/10.1099/mic.0.2007/010751-0

Longang, A., Buck, C., and Kirkwood, K. M. 2016. Halotolerance and effect of salt on hydrophobicity in hydrocarbon-degrading bacteria. Environmental Technology 37(9):1133-1140. https://doi.org/10.1080/09593330.2015.1102333

Maneerat, S. and Dikit, P. 2007. Characterization of cell-associated bioemulsifier from Myroides sp. SM1, a marine bacterium. Songklanakarin Journal of Science and Technology 29(3):769–779.

Marchal, R., Penet, S., Solano-Serena, F., and Vandecasteele, J. P. 2003. Gasoline and diesel oil biodegradation. Oil and Gas Science and Technolo-gy 58(4):441–448. https://doi.org/10.2516/ogst:2003027

Margesin, R. and Schinner, F. 2001. Biodegradation and bioremediation of hydrocarbons in extreme environments. Applied Microbiology and Bio-technology 56:650–663. https://doi.org/10.1007/s002530100701

Mikolasch, A., Omirbekova, A., Schumann, P., Reinhard, A., Sheikhany, H., Berzhanova, R., Mukasheva, T., and Schauer, F. 2024. Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan. Applied Microbiology and Biotechnology 108:189. https://doi.org/10.1007/s00253-024-13010-y

Mineev, V. G. 2001. Praktikum po agrokhimii. 689 p. Lomonosov Moscow University Press, Moscow. (In Russian)

Nazina, T. N., Shumkova, E. S., Sokolova, D. Sh., Babich, T. L., Zhurina, M. V., Xue, Y.-F., Osipov, G. A., Poltaraus, A. B., and Tourova, T. P. 2015. Identification of hydrocarbon-oxidizing Dietzia bacteria from petroleum reservoirs based on phenotypic properties and analysis of the 16S rRNA and gyrB genes. Microbiology (Moscow) 84(3):377–388. https://doi.org/10.7868/S0026365615030143

Netrusov, A. I. 2005. Praktikum po mikrobiologii. 608 p. Akademiia Publ., Moscow. (In Russian)

Oren, A. 2002. Halophilic microorganisms and their environments. 575 p. Kluwer Academic, Boston. https://doi.org/10.1007/0-306-48053-0

Oren, A. 2013. Life at high salt concentrations; pp. 263–282 in Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K. H., and Stackebrandt, E. (eds), The Prokaryotes. A handbook on the biology of bacteria: ecophysiology and biochemistry. Springer, New York. https://doi.org/10.1007/978-3-642-30123-0_57

Plakunov, V. K., Zhurina, M. V., and Belyaev, S. S. 2008. Resistance of the oil-oxidizing microorganism Dietzia sp. to hyperosmotic shock in reconstituted biofilms. Microbiology 77(5):515-522. https://doi.org/10.1134/S0026261708050019

Raymond, R. L. 1961. Microbial oxidation of n-paraffinic hydrocarbons. Development in Industrial Microbiology 2(1):23–32.

Riis, V., Kleinsteuber, S., and Babel, W. 2003. Influence of high salinities on the degradation of diesel fuel by bacterial consortia. Canadian Journal of Microbiology 49(11):713–721. https://doi.org/10.1139/W03-083

Rosenberg, M. 1984. Bacterial adherence to hydrocarbons: a useful technique for studying cell surface hydrophobicity. FEMS Microbiology Letters 22(3):289–295. https://doi.org/10.1111/j.1574-6968.1984.tb00743.x

Rubtsova, E. V., Kuyukina, M. S., and Ivshina, I. B. 2012. Effect of cultivation conditions on the adhesive activity of Rhodococcus cells towards n-hexadecane. Applied Microbiology and Biotechnology 48(5):452–459. https://doi.org/10.1134/S0003683812050110

Shivan, P. and Mugeraya, G. 2011. Halophilic bacteria and their compatible solutes — osmoregulation and potential applications. Current Science 100(10):1516–1521.

Sleator, R. D. and Hill, C. 2001. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiology Reviews 26(1):49–71. https://doi.org/10.1111/j.1574-6976.2002.tb00598.x

Tarfeen, N., Nisa, K. U., Hamid, B., Bashir, Z., Yatoo, A. M., Dar, M. A., Mohiddin, F. A., Amin, Z., Ahmad, R. A., and Sayyed, R. Z. 2022. Microbial remedi-ation: a promising tool for reclamation of contaminated sites with special emphasis on heavy metal and pesticide pollution: a review. Processes 10(7):1358. https://doi.org/10.3390/pr10071358

Tourova, T. P., Nazina, T. N., Mikhailova, E. M., Rodionova, T. A., Ekimov, A. N., Mashukova, A. V., and Poltaraus, A. B. 2008. AlkB homologs in thermophilic bacteria of the genus Geobacillus. Molecular Biology 42(2):217–226. https://doi.org/10.1134/S0026893308020076

Wang, X. B., Chi, C. Q., Nie, Y., Tang, Y. Q., Tan, Y., Wu, G., and Wu, X. L. 2011. Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain. Bioresource Technology 102(17):7755–7761. https://doi.org/10.1016/j.biortech.2011.06.009

Wang, X-B., Nie, Y., Tang, Y-Q., Wu, G., and Wu, X-L. 2013. n Alkane chain length alters Dietzia sp. strain DQ12-45-1b biosurfactant production and cell surface activity. Applied and Environmental Microbiology 79(1):400–402. https://doi.org/10.1128/AEM.02497-12

Xu, X., Liu, W., Tian, S., Wang, W., Qi, Q., Jiang, P., Gao, X., Li, F., Li, H., and Yu, H. 2018. Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: a perspective analysis. Frontiers in Microbiology 9:2885. https://doi.org/10.3389/fmicb.2018.02885

Zahir, H., Hamadi, F., Mallouki, B., Imziln, B., and Latrache, H. 2016. Effect of salinity on the adhesive power actinomycetes in soil. Journal of Materials and Environmental Science 7(9):3327–3333.

Zvyagintseva, I. S., Poglazova, M. N., Gotoeva, M. T., and Belyaev, S. S. 2001. Effect on the medium salinity on oil degradation by nocardioform bacteria. Microbiology 70(6):652–656. https://doi.org/10.1023/A:1013179513922