Thermoacidophilic bacteria isolated from Sarcheshmeh low-grade copper ore in chalcopyrite bioleaching from mineral tailing

Document Type : Research Paper


1 Department of Microbiology, Tehran North Branch, Islamic Azad University, Tehran, Iran.

2 School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran, Iran.

3 Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran.

4 Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.


This research has focused on isolating and identifying different thermoacidophilic bacteria from a Sarcheshmeh low-grade copper ore and evaluating their ability of copper bioleaching from the mineral tailing. After the isolation of the bacteria, molecular identification was carried out based on the 16S rRNA gene sequences and drawing the phylogenetic tree. Then, the effect of the pH, pulp density, and composition of the media on the copper bioleaching was determined using the identified bacteria. The isolated strain (Strain SCM1) belonged to Delftia acidovorans with a 95.73% of identity. The optimal condition for the copper bioleaching was reported in a medium consisting of sulfur (10 g/L), glucose (10 g/L), yeast extract (2 g/L), and mineral tailing (5% wt/vol) at the pH of 2.00 at 50°C. Under this condition, the highest amount of copper (83%) was bioleached. It proves that the lately isolated strain can be effectively employed in the copper bioleaching process.


Main Subjects

[1] Dong, Y., Lin, H., Wang, H., Mo, X., Fu, K., & Wen, H. (2011). Effects of ultraviolet irradiation on bacteria mutation and bioleaching of low-grade copper tailings. Minerals Engineering, 24(8), 870-875.
[2] Falagán, C., Grail, B.M., & Johnson, D.B. (2017). New approaches for extracting and recovering metals from mine tailings. Minerals Engineering, 106, 71-78.
[3] Nguyen, V.K., & Lee, J.U. (2015). A comparison of microbial leaching and chemical leaching of arsenic and heavy metals from mine tailings. Biotechnology and Bioprocess Engineering, 20(1), 91-99.
[4] Brierley, C.L., & Brierley, J.A. (2013). Progress in bioleaching: Part B: Applications of microbial processes by the minerals industries. Applied Microbiology and Biotechnology, 97(17), 7543-7552.
[5] Øvreås, L., & Torsvik, V. (1998). Microbial diversity and community structure in two different agricultural soil communities. Microbial Ecology, 36(3), 303-315.
[6] Huang, Z., Feng, S., Tong, Y., & Yang, H. (2019). Enhanced “contact mechanism” for the interaction of extracellular polymeric substances with low-grade copper-bearing sulfide ore in bioleaching by moderately thermophilic Acidithiobacillus caldus. Journal of Environmental Management, 242, 11-21.
[7] Jafari, M., Shafaei, S.Z., Abdollahi, H., Gharabaghi, M., & Chehreh Chelgani, S. (2018). Effect of Flotation Reagents on the Activity of L. Ferrooxidans. Mineral Processing and Extractive Metallurgy Review, 39(1), 34-43.
[8] Zhou, W.B., Li, K., Wang, Y.G., Zhang, L.J., Cheng, H.N., & Zhou, H.B. (2019). Influence of particle size on copper recovery from sulfide ore by the moderately thermophilic microorganisms. Metallurgical Research and Technology, 116(1),119. https://
[9] Prasidya, D.A., Wilopo, W., Warmada, I. W., & Retnaningrum, E. (2019). Optimization of manganese bioleaching activity and molecular characterization of indigenous heterotrophic bacteria isolated from the sulfuric area. Biodiversitas, 20(7), 1904-1909. 10.13057/biodiv/d200716
[10] Liu, R., Chen, J., Zhou, W., Cheng, H., & Zhou, H. (2019). Insight into the early-stage adsorption mechanism of moderately thermophilic consortia and intensified bioleaching of chalcopyrite. Biochemical Engineering Journal, 144, 40-47.
[11] Rodríguez, Y., Ballester, A., Blázquez, M.L., González, F., & Muñoz, J.A. (2003). New information on the pyrite bioleaching mechanism at low and high temperature. Hydrometallurgy, 71(1–2), 37-46.
[12] Konishi, Y., Tokushige, M., Asai, S., & Suzuki, T. (2001). Copper recovery from chalcopyrite concentrate by acidophilic thermophile Acidianus brierleyi in batch and continuous-flow stirred tank reactors. Hydrometallurgy. 59(2–3), 271-282.
[13] Huang, C., Qin,C., Feng, X., Liu, X., Yin, H., Jiang, L., Liang,Y., Liu, H., & Tao, J. (2018). Chalcopyrite bioleaching of an in situ leaching system by introducing different functional oxidizers. RSC Advances. 8, 37040-37049.
[14] Piervandi, Z., Khodadadi Darban, A., Mousavi, S.M., Abdollahy, M., Asadollahfardi, G., Funari, V., & Dinelli, E. (2019). Minimization of metal sulphides bioleaching from mine wastes into the aquatic environment. Ecotoxicology and Environmental Safety, 182,109443.
[15] Deng, S., Gu, G., Wu, Z., & Xu, X. (2017). Bioleaching of arsenopyrite by mixed cultures of iron-oxidizing and sulfur-oxidizing microorganisms. Chemosphere, 185, 403-411.
[16] Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. Journal of Molecular Biology, 3(2), 208-218.
[17] Lorenz, T.C. (2012). Polymerase chain reaction: Basic protocol plus troubleshooting and optimization strategies. Journal of Visualized Experiments, 63, 1-15.
[18] Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., & Wheeler, D.L. (2008). GenBank. Nucleic Acids Research, 36(1), 25-30.
[19] Felsenstein, J. (1985).Confidence Limits on Phylogenies: an Approach Using the Bootstrap. Evolution, 39(4), 783-791.
[20] Wei, D., Liu, T., Zhang, Y., Cai, Z., He, J., & Xu, C. (2018). Vanadium bioleaching behavior by Acidithiobacillus ferrooxidans from a vanadium-bearing shale. Minerals, 8(1), 1-12.
[21] Bampole, D.L., & Mulaba-Bafubiandi, A.F. (2018). The removal performance of silica and solid colloidal particles from chalcopyrite bioleaching solution: Effect of coagulant (Magnafloc set #1597) for predicting an effective solvent extraction. Engineering Journal, 22(5), 123-139.
[22] Graff, A., & Stubner, S. (2003). Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil. Systematic and Applied Microbiology, 26(3), 445-452.
[23] Funari, R., Ripa, R., Söderström, B., Skoglund, U., & Shen, A.Q. (2019). Detecting Gold Biomineralization by Delftia acidovorans Biofilms on a Quartz Crystal Microbalance. ACS Sensors, 4(11), 3023-3033.
[24] Das, S., Natarajan, G., & Ting, Y.P. (2017). Bio-extraction of precious metals from urban solid waste. AIP Conference Proceedings, 2017Jan.
[25] Natarajan, V.P., Zhang, X., Morono, Y., Inagaki, F., & Wang, F. (2016). A modified SDS-based DNA extraction method for high quality environmental DNA from seafloor environments. Frontiers in Microbiology, 7, 986.
[26] Abdollahi, H., Shafaei. S.Z., Noaparast, M., & Manafi, Z. (2017). Mixed moderate thermophilic bioleaching of Cu, Mo and Re from molybdenite concentrate: effects of silver ion, medium and energy sources. International journal of mining and Geo-engineering, 51(2), 151-159.
[27] Wang, Y., Chen, X., & Zhou, H. (2018). Disentangling effects of temperature on microbial community and copper extraction in column bioleaching of low grade copper sulfide. Bioresource Technology, 268, 480-487.
[28] Mousavi, S.M., Yaghmaei, S., Vossoughi, M., Jafari, A., & Hoseini, S.A. (2005). Comparison of bioleaching ability of two native mesophilic and thermophilic bacteria on copper recovery from chalcopyrite concentrate in an airlift bioreactor. Hydrometallurgy, 80(1-2), 139-144.
[29] Zhang, L., Zhou, W., Li, K., Mao, F., Wan, L., Chen, X., Qiu, G. (2015). Synergetic effects of Ferroplasma thermophilum in enhancement of copper concentrate bioleaching by Acidithiobacillus caldus and Leptospirillum ferriphilum. Biochemical Engineering Journal, 93, 142-150.
[30] Jørgensen, N.O.G., Brandt, K.K., Nybroe, O., & Hansen, M. (2009). Delftia lacustris sp. nov., a peptidoglycandegrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology, 59(9), 2195-2199.
[31] Yin, S.H., Wang, L.M., Wu, A.X., Chen, X., & Yan, R.F. (2019). Research progress in enhanced bioleaching of copper sulfides under the intervention of microbial communities. International Journal of Minerals, Metallurgy and Materials, 26(11), 1337-1350.
[32] Shiers, D.W., Collinson, D.M., & Watling, H.R. (2016). Life in heaps: a review of microbial responses to variable acidity in sulfide mineral bioleaching heaps for metal extraction. Research in Microbiology, 167(7), 576-586.
[33] Zhou, W., Zhang, L., Peng, J., Ge, Y., Tian, Z., Sun, J., Zhou, H. (2019). Cleaner utilization of electroplating sludge by bioleaching with a moderately thermophilic consortium: A pilot study. Chemosphere, 232, 345-355.
[34] Falagán, C., & Johnson, D.B. (2018). The significance of pH in dictating the relative toxicities of chloride and copper to acidophilic bacteria. Research in Microbiology, 169(10), 552-557.
[35] Pecina, E.T., Castillo, P., Martinez, D., & Orrantia, E. (2010). Biooxidation of an auriargentiferous arsenical pyrite concentrate by means of mesophilic and thermophilic bacteria. Minerals and Metallurgical Processing, 27(4), 212-218.
[36] Do Nascimento, D.N.O., Lucheta, A.R., Palmieri, M.C., Do Carmo, A.L.V., Silva, P.M.P., Ferreira, R.V.P., Alves, J.O. (2019). Bioleaching for copper extraction of marginal ores from the Brazilian Amazon region. Metals, 9(1), 1-13. https://
[37] Noei, S.B., Sheibani, S., Rashchi, F., & Mirazimi, S.M.J. (2017). Kinetic modeling of copper bioleaching from low-grade ore from the Shahrbabak Copper Complex. International Journal of Minerals, Metallurgy and Materials, 24(6), 611-620.
[38] Mikoda, B., Potysz, A., & Kmiecik, E. (2019). Bacterial leaching of critical metal values from Polish copper metallurgical slags using Acidithiobacillus thiooxidans. Journal of Environmental Management, 236, 436-445.
[39] Nascimento, D.N.O., Lucheta, A.R., Palmieri, M.C., Carmo, A.L.V., Silva, P.M.P., Pádua Ferreira, R.V., Junca, E., Grillo, F.F.,& Alves, J.O. (2019). Bioleaching for Copper Extraction of Marginal Ores from the Brazilian Amazon Region. Metals. 9, 81.
[40] Panyushkina, A., Fomchenko, N., Babenko, V., & Muravyov, M. (2021). Effect of Temperature on Biobeneficiation of Bulk Copper-Nickel Concentrate with Thermoacidophilic Microbial Communities. Metals. 11, 1969.
[41] Tipre, D.R., Vora, S.B., & Dave, S.R. (2004). Medium optimization for bioleaching of metals from Indian bulk polymetallic concentrate. Indian Journal of Biotechnology, 3(1), 86-91.
[42] Seidel, A., Zimmels, Y., & Armon, R. (2001). Mechanism of bioleaching of coal fly ash by Thiobacillus thiooxidans. Chemical Engineering Journal, 83(2), 123-130. https://
[43] Wang, Y., Zeng, W., Qiu, G., Chen, X., & Zhou, H. (2014). A Moderately Thermophilic Mixed Microbial Culture for Bioleaching of Chalcopyrite Concentrate at High Pulp Density. Applied and Environmental Microbiology, 80(2), 741-750.
[44] Akcil, A., Ciftci, H., & Deveci, H. (2007). Role and contribution of pure and mixed cultures of mesophiles in bioleaching of a pyritic chalcopyrite concentrate. Minerals Engineering, 20(3), 310-318.
[45] Shaikh Shafikh, M., Ahmed, A.A., & Ahmed, S.A. (2018). Impact of pulp density on extraction of metals, by Acidithiobacillus ferrooxidans and Pseudomonas fluorescens from bauxite ore. Journal of Pure and Applied Microbiology, 12(3), 1647-1654.