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Improved uranium bioleaching in brackish environments via microbial consortium using RSM based modelling and optimization
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  • Published: 18 February 2026

Improved uranium bioleaching in brackish environments via microbial consortium using RSM based modelling and optimization

  • Maryam Shoja1,
  • Parisa Mohammadi1,
  • Parisa Tajer-Mohammad-Ghazvini2 &
  • …
  • Hassan Zare-Tavakoli2 

Scientific Reports , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Applied microbiology
  • Environmental biotechnology
  • Environmental microbiology

Abstract

Bioleaching is a prominent method among eco-friendly techniques. The efficiency of bioleaching is reduced by the presence of brackish water. Moreover, it has been reported that the most successful bioleaching systems are those that include both autotrophic and heterotrophic microorganismes. This research focuses on enhancing uranium bioleaching in brackish waters using the halotolerant bacterium Acidithiobacillus ferrooxidans strain THA4 and the fungus Rhodotorula toruloides strain IR-1395. The experimental data were modeled by the Response Surface Methodology (RSM) approach. The suggested model for uranium extraction in a brackish environment using microorganisms demonstrated an alignment with the experimental data, with a correlation coefficient of R2 = 0.94. The results showed that the amount of uranium bioleaching by the consortium increased by 24.22%, compared to the bacterium alone under the optimal conditions suggested by the software. The study employed SEM–EDS to investigate the morphological changes in ore samples exposed to the microorganisms. The findings offer insights into the relationship dynamics between acidophilic bacteria and heterotrophic yeasts in uranium bioleaching of brackish waters. Finally, this study has improved biohydrometallurgical methods for uranium extraction from low-grade ores, especially in saline and low-resources conditions.

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Data availability

All data generated or analyzed during this study are included in this article. The 16S rDNA sequence of Acidithiobacillus ferrooxidans strain THA4 had been deposited in the National Center for Biotechnology Information (NCBI) GenBank with the accession number PV981793 (https://www.ncbi.nlm.nih.gov/nuccore/PV981793). The 18S rDNA sequence and large subunit rDNA sequence of Rhodotorula toruloides strain IR-1395 had been deposited in the National Center for Biotechnology Information (NCBI) GenBank with the accession number KX452402.1 and MN752210.1, respectively (https://www.ncbi.nlm.nih.gov/nuccore/KX452402 and https://www.ncbi.nlm.nih.gov/nuccore/MN752210).

References

  1. Tavakoli, H. Z., Abdollahy, M., Ahmadi, S. & Darban, A. K. Kinetics of uranium bioleaching in stirred and column reactors. Miner. Eng. 111, 36–46 (2017).

    Google Scholar 

  2. Kaksonen, A. H., Lakaniemi, A.-M. & Tuovinen, O. H. Acid and ferric sulfate bioleaching of uranium ores: A review. J. Clean. Prod. 264, 121586 (2020).

    Google Scholar 

  3. Pradhan, N., Nathsarma, K., Rao, K. S., Sukla, L. & Mishra, B. Heap bioleaching of chalcopyrite: A review. Miner. Eng. 21(5), 355–365 (2008).

    Google Scholar 

  4. Chen, W., Tang, H. & Yin, S. Bioleaching of low-grade copper sulfide enhanced by nutrients from sterilized medical waste. Process Saf. Environ. Protect. 188, 1527–1535 (2024).

    Google Scholar 

  5. Nagpal, S., Dahlstrom, D. & Oolman, T. Effect of carbon dioxide concentration on the bioleaching of a pyrite–arsenopyrite ore concentrate. Biotechnol. Bioeng. 41(4), 459–464 (1993).

    Google Scholar 

  6. Barron, J. L. & Lueking, D. R. Growth and maintenance of Thiobacillus ferrooxidans cells. Appl. Environ. Microbiol. 56(9), 2801–2806 (1990).

    Google Scholar 

  7. Schippers, A., Hetz, S. A. & Ostertag-Henning, C. Laterite ore processing with hydrogen via mild chemical pressure leaching or bioleaching. Hydrometallurgy https://doi.org/10.1016/j.hydromet.2025.106447 (2025).

    Google Scholar 

  8. Khetwunchai, N. et al. Enhanced bioleaching of copper and gold from waste printed circuit boards: Stepwise process, pretreatment strategies, metabolomics analysis, and the role of N8-acetylspermidine. Process Saf. Environ. Protect. 194, 289–305 (2025).

    Google Scholar 

  9. Dew, D. W., Lawson, F. & Broadhurst, J. L. The bioleaching of sulfide minerals with emphasis on copper sulfides a review. Hydrometallurgy 47, 155–170 (1997).

    Google Scholar 

  10. Rea, S. et al. Salt-tolerant microorganisms potentially useful for bioleaching operations where fresh water is scarce. Miner. Eng. 75, 126–132 (2015).

    Google Scholar 

  11. Simmons, S. F. & Norris, P. R. Acidophilic microorganisms and their interactions with minerals in saline environments. Extremophiles 6(6), 551–559 (2002).

    Google Scholar 

  12. Noguchi, H. & Okibe, N. The role of bioleaching microorganisms in saline water leaching of chalcopyrite concentrate. Hydrometallurgy 195, 105397 (2020).

    Google Scholar 

  13. Shivanand, P. & Mugeraya, G. Halophilic microorganisms and their adaptation mechanisms. Crit. Rev. Microbiol. 37(4), 315–334 (2011).

    Google Scholar 

  14. Oren, A. Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes. Front. Microbiol. 4, 315 (2013).

    Google Scholar 

  15. Graziano, G. & Merlino, A. Molecular bases of protein halotolerance. Biochimica et Biophysica Acta (BBA) 1844(4), 850–858 (2014).

    Google Scholar 

  16. Fournier, D., Lemieux, R. & Couillard, D. Essential interactions between Thiobacillus ferrooxidans and heterotrophic microorganisms during a wastewater sludge bioleaching process. Environ. Pollut. 101(2), 303–309 (1998).

    Google Scholar 

  17. Gu, X.-Y. & Wong, J. W. Degradation of inhibitory substances by heterotrophic microorganisms during bioleaching of heavy metals from anaerobically digested sewage sludge. Chemosphere 69(2), 311–318 (2007).

    Google Scholar 

  18. Zheng, G., Zhou, L. & Wang, S. An acid-tolerant heterotrophic microorganism role in improving tannery sludge bioleaching conducted in successive multibatch reaction systems. Environ. Sci. Technol. 43(11), 4151–4156 (2009).

    Google Scholar 

  19. Tavakoli, H. Z., Abdollahy, M., Ahmadi, S. & Darban, A. K. Enhancing recovery of uranium column bioleaching by process optimization and kinetic modeling. Trans. Nonferrous Met. Soc. China 27(12), 2691–2703 (2017).

    Google Scholar 

  20. Bomberg, M., Mäkinen, J., Salo, M. & Kinnunen, P. High diversity in iron cycling microbial communities in acidic, iron‐rich water of the Pyhäsalmi Mine, Finland. Geofluids 2019(1), 7401304 (2019).

    Google Scholar 

  21. Piroeva, I. et al. A simple and rapid scanning electron microscope preparative technique for observation of biological samples: application on bacteria and DNA samples. Bulg. Chem. Commun 45(4), 510–515 (2013).

    Google Scholar 

  22. Csonka, L. N. Physiological and genetic responses of bacteria to osmotic stress. Microbiol. Rev. 53(1), 121–147 (1989).

    Google Scholar 

  23. Kieft, T. L. & Spence, S. D. Osmoregulation in Thiobacillus ferrooxidans: Stimulation of iron oxidation by proline and betaine under salt stress. Curr. Microbiol. 17, 255–258 (1988).

    Google Scholar 

  24. Guo, X. et al. Role of proline biosynthesis in Acidithiobacillus caldus under salt stress. J. Bacteriol. 195, 4421–4429 (2013).

    Google Scholar 

  25. Zammit, C. M. et al. Bioleaching in brackish waters—effect of chloride ions on the acidophile population and proteomes of model species. Appl. Microbiol. Biotechnol. 93, 319–329 (2012).

    Google Scholar 

  26. Simmons, S. & Norris, P. Acidophiles of saline water at thermal vents of Vulcano, Italy. Extremophiles 6, 201–207 (2002).

    Google Scholar 

  27. Sand, W. et al. Microbial mechanisms for metal leaching in acidic environments. Hydrometallurgy 59(3), 159 (2001).

    Google Scholar 

  28. Zheng, X. & Li, D. Interaction of Acidithiobacillus ferrooxidans, Rhizobium phaseoli and Rhodotorula sp. in bioleaching process based on Lotka-Volterra model. Electron. J. Biotechnol. 22, 90–97 (2016).

    Google Scholar 

  29. Ingledew, W. J. Thiobacillus ferrooxidans the bioenergetics of an acidophilic chemolithotroph. Biochimica et Biophysica Acta (BBA) 683(2), 89–117 (1982).

    Google Scholar 

  30. Salinas, E. et al. Removal of cadmium and lead from dilute aqueous solutions by Rhodotorula rubra. Bioresour. Technol. 72(2), 107–112 (2000).

    Google Scholar 

Download references

Acknowledgements

This manuscript was a part of the PhD. thesis by M. Shoja, under the supervision of Dr. P. Mohammadi and Dr. P. Tajer-Mohammad-Ghazvini; and advi¬sory of H. Zare-Tavakoli. The authors would like to thank Alzahra University and also Nuclear Science and Technology Research Institute, Tehran, Iran for their support through this study.

Author information

Authors and Affiliations

  1. Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran

    Maryam Shoja & Parisa Mohammadi

  2. Nuclear Fuel Cycle Research School, Nuclear Science and Technology Research Institute, Tehran, Iran

    Parisa Tajer-Mohammad-Ghazvini & Hassan Zare-Tavakoli

Authors
  1. Maryam Shoja
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  2. Parisa Mohammadi
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  3. Parisa Tajer-Mohammad-Ghazvini
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  4. Hassan Zare-Tavakoli
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Contributions

The manuscript was a part of the PhD. thesis by M. S. All the authors contributed to the conception and design of the study. M. S.: conducting experiments, writing (original draft preparation). Dr. P.M.: writing (review and editing), supervision. Dr. P. T-M-G.: writing (review and editing), supervision, software. Dr. H. Z-T.: adviser. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Parisa Mohammadi or Parisa Tajer-Mohammad-Ghazvini.

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Cite this article

Shoja, M., Mohammadi, P., Tajer-Mohammad-Ghazvini, P. et al. Improved uranium bioleaching in brackish environments via microbial consortium using RSM based modelling and optimization. Sci Rep (2026). https://doi.org/10.1038/s41598-026-39700-3

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  • Received: 22 May 2025

  • Accepted: 06 February 2026

  • Published: 18 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-39700-3

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Keywords

  • Biohydrometallurgy
  • Experimental design
  • Microbial collaboration
  • Saline water
  • Uranium ore
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