Prospects and problems of application of acidophilic bacteria Acidithiobacillus ferrooxidans in the extraction of precious metals by bioleaching

The article reviews the published scientific information on application of acidophilic bacteria Acidithiobacillus ferrooxidans, promising for the practical application in bioleaching of precious metals, and analyzes problems connected with such application. Biogeotechnologies are suitable for recovery of precious metals from raw materials with low content of strategic metals, from low-grade ore, refuse heaps and solid waste dumps. Bioleaching using microorganisms as the main metal-leach agents is an alternative method of metal smelting, when ore contains less than 1% of target metals, and of classical leaching, as a method of anthropogenic load reduction in the metal production area. The use of strict iron- and sulfur-oxidizing acidophiles A. ferrooxidans is based on the known approaches to processing of sulfide mineral raw materials (for instances, ores and concentrates of precious metals), and on the ability of bacteria to interact differently with mineral surface, which leads to transition of metals to pregnant solutions. A promising area of biohydrometallurgy is the application of A. ferrooxidans in recovery of metals from low-grade minerals of different genesis. The review embraces the issues of tolerance of A. ferrooxidans to heavy metals and the degree of knowledge on molecular genetic manipulation relative to A. ferrooxidans. The discussed material can be interesting to specialists in the fields of microbiology and biohydrometallurgy, in terms of analyzing physiological characteristics of A. ferrooxidans for their enhanced efficiency in processing of natural and man-made mineral raw materials. 

Yachkula A. A. Prospects and problems of application of acidophilic bacteria Acidithiobacillus ferrooxidans in the extraction of precious metals by bioleaching. MIAB. Mining Inf. Anal. Bull. 2026;(10):35-52. [In Russ]. DOI: 10.25018/0236_1493_2026_10_0_35.

This work was supported by the Ministry of Science and Higher Education of the Russian Federation under State Assignment FMRM-2026-0020.

A.A. Yachkula, Junior Researcher, Graduate Student, Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center «Pushchino Scientific Center for Biological Research, Russian Academy of Sciences», e-mail: a.yachkula@pbcras.ru, ORCID ID: 0000-0002-7396-8931.

1. Kryukov V. A., Yacenko V. A., Kryukov Yа. V. Rare еarth industry – how to tacke advantage of opportunities. Russian Mining Industry Journal. 2020, vol. 5, pp. 68—84. [In Russ]. DOI: 10.30686/1609-9192-2020-5-68-84.

2. Ratsional'noe ispol'zovanie vtorichnykh mineral'nykh resursov v usloviyakh ekologizatsii i vnedreniya nailuchshikh dostupnykh tekhnologiy: monografiya. Kollektiv avtorov; pod nauch. red. F.D. Larichkina, V.A. Knysha [Rational use of secondary mineral resources in the context of greening and the introduction of the best available technologies: monografiya, under scientific editorship Larichkina F. D., Knysha V. A.], Apatity, 2019, 252 p. DOI: 10.37614/978.5.91137.417.4.

3. Kumar A., Lima A. T., Kirkelund G. M., Jensen P. E., Ottosen L. M., Funari V., Shemi A., Ndlovu S., Gomes H. I. Bioleaching: from natural ores to urban mines for sustainability, circularity, and carbon neutrality. Resources, Conservation and Recycling. 2026, vol. 227, article 108746. DOI: 10.1016/j.resconrec.2025.108746.

4. Blinov N. I., Fesak A. A. Comparison of methods for leaching precious metals from refractory ores. Pererabotka prirodnogo i tekhnogennogo syr'ya: sbornik nauchnykh trudov studentov, magistrantov, aspirantov i molodykh uchenykh Instituta metallurgii i khimicheskoy tekhnologii im. S.B. Leonova [Processing of natural and man-made raw materials: collection of scientific papers of students, undergraduates, postgraduate students and young researchers of the S.B. Leonov Institute of metallurgy and chemical technology], Irkutsk, 2016, 300 p.

5. Watling H. R. The bioleaching of sulphide minerals with emphasis on copper sulphides — A review. Hydrometallurgy. 2006, vol. 84, no. 1-2, pp. 81—108. DOI: 10.1016/j.hydromet.2006.05.001.

6. Yаgafarova G. G., Kutliahmetov A. N., Safarova V. I., Kubareva S. Yu. The role of thiobacteria in the leaching of metals from waste dumps at the Uchaly Mining and Processing Plant. Georesources. 2012, no. 6 (48), pp. 84—86. [In Russ].

7. Wang X., Ma L., Wu J., Xiao Y., Tao J., Liu X. Effective bioleaching of low-grade copper ores: Insights from microbial cross experiments. Bioresource Technology. 2020, vol. 308, article 123273. DOI: 10.1016/j.biortech.2020.123273.

8. Jones S., Santini J. M. Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms. Essays in Biochemistry. 2023, vol. 67, no. 4, pp. 685—699. DOI: 10.1042/EBC20220257.

9. Murav'yov M. I., Panyushkina A. E., Melamud V. S., Bulaev A. G., Fomchenko N. V. Chemical leaching of bulk sulfide concentrates with a solution of ferric sulfate. Applied biochemistry and microbiology. 2021, vol. 57, no. 4, pp. 380—387. [In Russ]. DOI: 10.31857/S0555109921040115.

10. Levenspiel O. Chemical Reaction Engineering. 2nd ed. N.Y.: Wiley, 1972, 578 p.

11. Murav'yov M. I., Fomchenko N. V. Chemical leaching of low-grade zinc concentrate with a trivalent iron biosolution. Applied biochemistry and microbiology. 2019, vol. 55, no. 4, pp. 396—402. [In Russ]. DOI: 10.1134/S0555109919040123.

12. Fomchenko N. V., Murav'yov M. I. Bioleaching of sulphide concentrates with different copper and zinc contents and assessment of the quality of the resulting precipitates. Applied biochemistry and microbiology. 2020, vol. 56, no. 4, pp. 366—372. [In Russ].

13. Rohwerder T., Gehrke T., Kinzler K., Sand W. Bioleaching review part A: progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation. Applied Microbiology and Biotechnology. 2003, vol. 63, no. 3, pp. 239—248. DOI: 10.1007/s00253-003-1448-7.

14. Vera M., Schippers А., Hedrich S., Sand W. Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation — part A. Applied Microbiology and Biotechnology. 2022, vol. 106, pp. 6933—6952. DOI: 10.1007/s00253-022-12168-7.

15. Rodríguez Y., Ballester A., Blázquez M. L., González F., Muñoz J. A. Study of bacterial attachment during the bioleaching of pyrite, chalcopyrite, and sphalerite. Geomicrobiology Journal. 2003, vol. 20, no. 2, pp. 131—141. DOI: 10.1080/01490450303880. 

16. Tributch H. Direct versus indirect bioleaching. Hydrometallurgy. 2001, vol. 59. pp. 177—185. DOI: 10.1016/S0304-386X(00)00181-X.

17. Bomberg M., Miettinen H., Hajdu-Rahkama R., Lakaniemi A.-M., Anacki W., Witecki K., Puhakka J. A., Ineich T., Slabbert W., Kinnunen P. Indirect in situ bioleaching is an emerging tool for accessing deeply buried metal reserves, but can the process be managed? — A case study of copper leaching at 1 km depth. Environmental Technology & Innovation. 2023, vol. 32, article 103375. DOI: 10.1016/j.eti.2023.103375.

18. Sharipov S. Sh., Mukhiddinov B. F. Bacterial leaching of sulfide flotation concentrates. Universum: technical sciences. 2020, no. 12-4 (81), pp. 97—100. [In Russ]. DOI: 10.32743/UniTech.2020.81.12-4.97-100.

19. Silverman M. P., Lundgren D. G. Studies on the chemoautotrophic iron bacterium Ferrobacillus ferrooxidans. I. An improved medium and a harvesting procedure for securing high cell yields. Journal of Bacteriology. 1959, vol. 77, no. 5, pp. 642—647.

20. Pronk Ya. T., Van Dejken J. P., Bos P., Kuenen J. G. Patent RU 2099412. 20.12.1997. [In Russ].

21. Pronk J. T., Meijer W. M., Hazeu W., van Dijken J. P., Bos P., Kuenen J. G. Growth of Thiobacillus ferrooxidans on formic acid. Applied and Environmental Microbiology. 1991, vol. 57, no. 7, pp. 2057—2062. DOI: 10.1128/aem.57.7.2057-2062.1991.

22. Gumulya Y., Boxall N. J., Khaleque H. N., Santala V., Carlson R. P., Kaksonen A. H. In a quest for engineering acidophiles for biomining applications: challenges and opportunities. Genes (Basel). 2018, vol. 9, no. 2, article 116. DOI: 10.3390/genes9020116.

23. Valdés J., Pedroso I., Quatrini R., Dodson R. J., Tettelin H., Blake R., Eisen J. A., Holmes D. S. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics. 2008, vol. 9, article 597. DOI: 10.1186/1471-2164-9-597.

24. Yachkula A., Rozova О., Abashina T., Vainshtein M., Grouzdev D., Bulaev A. Attempts to stimulate leaching activity of Acidithiobacillus ferrooxidans strain TFBk. Minerals. 2022, vol. 12, article 1051. DOI: 10.3390/min12081051.

25. Abashina T., Yachkula A., Shaikin A., Vainshtein M. Approaches to improve the bioleaching of arsenopyrite flotation concentrate with Acidithiobacillus ferrooxidans: comparison of two strains of different origin. Engineering Proceedings. 2024, no. 67, article 60. DOI: 10.3390/engproc2024067060.

26. Yachkula A., Kuvichkina T., Zvonarev A., Abashina T., Reshetilov A., Vainshtein M. Extremophilic bacteria Acidithiobacillus ferrooxidans: substrate preference and response to arsenic compounds evaluated by oxygen consumption. Microbiology. 2026, vol. 95, no. 2, pp. 243—250. 

27. Kioresku A. V. Intensification of bacterial-chemical leaching of nickel, copper and cobalt from sulfide ore using microwave radiation. Journal of Mining Institute. 2019, vol. 239, pp. 528—535. [In Russ]. DOI: 10.31897/PMI.2019.5.528.

28. Dash J., Ojha R., Pradhan D. Progress in bioleaching and its mechanism: a short review. Discover Environment. 2025, vol. 3, article 238. DOI: 10.1007/s44274-025-00454-w.

29. Telyakov N. M., Dar'in A. A., Luganov V. A. Prospects for the application of biotechnology in metallurgy and enrichment. Journal of Mining Institute. 2016, vol. 217, pp. 113—124. [In Russ].

30. Shaihova D. R. Prospects for the use of Acidithiobacillus ferrooxidans in bioleaching of metals from industrial waste. Minerals and Mining Engineering. 2019, no. 6, pp. 90—97. [In Russ]. DOI: 10.21440/0536-1028-2019-6-90-97.

31. Lane K. R., Jones S. E., Osborne T. H., Geller-McGrath D., Nwaobi B. C., Chen L., Thomas B. C., Hudson-Edwards K. A., Banfield J. F., Santini J. M. Bioleaching microbial community metabolism and composition driven by copper sulphide mineral type. Environmental Microbiology Reports. 2025, vol. 17, no. 6, article 70261. DOI: 10.1111/1758-2229.70261. 

32. Wang X., Ma L., Wu J., Xiao Yu., Tao J., Liu X. Effective bioleaching of low-grade copper ores: Insights from microbial cross experiments. Bioresource Technology. 2020, vol. 308, article 123273. DOI: 10.1016/j.biortech.2020.123273.

33. Saldaña M., Jeldres M., Galleguillos Madrid F. M., Gallegos S., Salazar I., Robles P., Toro N. Bioleaching modeling — A review. Materials (Basel). 2023, vol. 16, no. 10, article 3812. DOI: 10.3390/ma16103812.

34. Adamov E. V., Panin V. V. Metal biotechnology: reality and prospects. Journal of Mining Institute. 2005, vol. 165, pp. 10—11. [In Russ].

35. Krylova L. N., Kim E. A., Balanceva E. B., Kim A. K., Starodubceva V. D.  Patent RU  2478127  C1. 27.03.2013. [In Russ].

36. Kanaev A. T., Baimyrzaev K. M., Semenchenko G. V., Kanaeva Z. K., Sovetova N. Zh., Tokpaev K. M., Shemsheeva Zh. B., Umirbekova Zh. T., Amanbaeva U. I. Large-scale laboratory bacterial-chemical leaching of gold from ore of the Bakyrchik deposit. Advances in current natural sciences. 2017, no. 3, pp. 14—18. [In Russ].

37. Navarro C. A., von Bernath D., Jerez C. A. Heavy metal resistance strategies of acidophilic bacteria and their acquisition: importance for biomining and bioremediation. Biological Research. 2013, no. 46, pp. 363—371. DOI: 10.4067/S0716-97602013000400008.

38. Moya-Beltrán A., Beard S., Rojas-Villalobos C., Issotta F., Gallardo Y., Ulloa R., Giaveno A., Degli Esposti M., Johnson D. B., Quatrini R. Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions. ISME Journal. 2021, vol. 15, no. 11, pp. 3221—3238. DOI: 10.1038/s41396-021-00995-x.

39. Liu Z., Guiliani N., Appia-Ayme C., Borne F., Ratouchniak J., Bonnefoy V. Construction and characterization of a recA mutant of Thiobacillus ferrooxidans by marker exchange mutagenesis. Journal of Bacteriology. 2000, vol. 182, no. 8, pp. 2269—2276. DOI: 10.1128/JB.182.8.2269-2276.2000.

40. Liu W., Lin J., Pang X., Cui S., Mi S., Lin J. Overexpression of rusticyanin in Acidithiobacillus ferrooxidans ATCC19859 increased Fe(II) oxidation activity. Current Microbiology. 2011, vol. 62, no. 1, pp. 320—324. DOI: 10.1007/s00284-010-9708-0.

41. Ramos-Zúñiga J., Gallardo S., Martínez-Bussenius C., Norambuena R., Navarro C. A., Paradela A., Jerez C. A. Response of the biomining Acidithiobacillus ferrooxidans to high cadmium concentrations. Journal of Proteomics. 2019, vol. 198, pp. 132—144. DOI: 10.1016/j.jprot.2018.12.013.

42. Jiang Y., Wu R., Zhang W., Xin F., Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends in Biotechnology. 2023, vol. 41, no. 11, pp. 1430—1441. DOI: 10.1016/j.tibtech.2023.05.008.

43. Großkopf T., Soyer O. S. Synthetic microbial communities. Current Opinion in Microbiology. 2014, vol. 18, pp. 72—77. DOI: 10.1016/j.mib.2014.02.002.

44. Brune K. D., Bayer T. S. Engineering microbial consortia to enhance biomining and bioremediation. Frontiers in Microbiology. 2012, vol. 3, article 203. DOI: 10.3389/fmicb.2012.00203.

45. Boase К., Santini T., Watkin E. Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia. Frontiers in Microbiology. 2024, vol. 15, article 1308797. DOI: 10.3389/fmicb.2024.1308797.

46. Topychkanova E. I., Dementieva N. A., Mullov V. M., Chikin A. Yu. Optimization of low-grade refractory gold ore processing. Transbaikal state university journal. 2024, vol. 30, no. 3, pp. 89—100. [In Russ]. DOI: 10.21209/2227-9245-2024-30-3-89-100.