Microbial and metabolic leaching mechanisms for rare earth recovery from clay minerals

Abstract

This study systematically investigated the leaching efficacy and mechanisms of La³⁺ and Y³⁺ from the clay minerals kaolinite and halloysite by Aspergillus niger, Acidithiobacillus ferrooxidans, and typical metabolites (citric acid and protease). The results indicated that nearly complete leaching of rare earth ions was achieved by A. niger, A. ferrooxidans, their fermentation broths, and citric acid. A. niger dissolves rare earth ions mainly by secreting organic acids, which form soluble complexes to promote mineral dissolution and increase ion-exchange release. In contrast, A. ferrooxidans oxidizes elemental sulfur to generate sulfuric acid, significantly reducing the system’s pH and enhancing the leaching process. However, both microorganisms adsorbed free rare earth ions during the later stages of leaching, leading to a decrease in their concentrations in the solution. Citric acid significantly improved the solubility of rare earth elements through complexation, whereas proteases showed relatively poor leaching efficiency for clay minerals. Phase composition and surface functional group analyses revealed notable changes in the O-H and C=O groups of kaolinite and halloysite after treatment with microbes and their metabolites, which increased mineral reactivity. This research provides a theoretical basis and technical support for the green and efficient recovery of rare earth resources from clay minerals.

Keywords

bioleaching / Aspergillus niger / Acidithiobacillus ferrooxidans / typical metabolites / clay minerals

References

[1] Asadollahzadeh M, Torkaman R, Torab-Mostaedi M. Extraction and separation of rare earth elements by adsorption approaches: Current status and future trends [J]. Separation & Purification Reviews, 2021, 50(4): 417-444

[2] Nguyen Q L, Lai H N, Nguyen H T M, et al.. Explainable artificial intelligence for predicting rare earth elements leaching from secondary resources [J]. Journal of Hazardous Materials, 2025, 496: 139479

[3] Ghorbani Y, Ilankoon I M S K, Dushyantha N, et al.. Rare earth permanent magnets for the green energy transition: Bottlenecks, current developments and cleaner production solutions [J]. Resources, Conservation and Recycling, 2025, 212: 107966

[4] Zhao C-x, Yang B-j, Hu S, et al.. Bioleaching and mechanism of ion-adsorption type rare earth ores and tailings using [J]. Hydrometallurgy, 2025, 236: 106495

[5] Herrington R. Mining our green future [J]. Nature Reviews Materials, 2021, 6(6): 456-458

[6] Ali S H, Giurco D, Arndt N, et al.. Mineral supply for sustainable development requires resource governance [J]. Nature, 2017, 543(7645): 367-372

[7] Wang S-s, Zhong C, Shen C, et al.. Selective-crystallization strategy for the separation of rare earth elements: A minireview [J]. Coordination Chemistry Reviews, 2025, 537: 216686

[8] Yan Q-t, Yang Z-m, Chen Z-liang. Recent advances in microbial nanomaterials/nanoparticles synthesis and rare earth elements recovery from rare earth mine wastewater: A review [J]. Chemical Engineering Journal, 2025, 510: 161647

[9] Xiang H-r, Yang Z-h, Liu X-y, et al.. Advancements in functional adsorbents for sustainable recovery of rare earth elements from wastewater: A comprehensive review of performance, mechanisms, and applications [J]. Advances in Colloid and Interface Science, 2025, 338: 103403

[10] Li L-q, Liu C-h, Zhang H-p, et al.. The enrichment of rare earth from magnesium salt leaching solution of ion-adsorbed type deposit: A waste-free process for removing impurities [J]. Journal of Environmental Management, 2022, 310: 114743

[11] Xie M-y, Yang F, Yang L-y, et al.. Highly efficient separation and recovery of heavy rare earths by ((dioctylamino)methyl)phenylphosphinic acid [J]. Separation and Purification Technology, 2025, 364: 132335

[12] He Q, Qiu J, Chen J-f, et al.. Progress in green and efficient enrichment of rare earth from leaching liquor of ion adsorption type rare earth ores [J]. Journal of Rare Earths, 2022, 40(3): 353-364

[13] Azimi G. Technological advancements in rare earth elements recovery from ionic clays: A comprehensive review [J]. Hydrometallurgy, 2025, 231: 106414

[14] Shi T, Li M-c, Wei G-s, et al.. Distribution patterns of microeukaryotic community between sediment and water of the Yellow River Estuary [J]. Current Microbiology, 2020, 77(8): 1496-1505

[15] Huang S-x, Li Z-h, Yu J-x, et al.. Vertical distribution and occurrence state of the residual leaching agent (ammonium sulfate) in the weathered crust elution-deposited rare earth ore [J]. Journal of Environmental Management, 2021, 299: 113642

[16] Chen X, Chen J-f, Li J-q, et al.. Strengthening rare earth and inhibiting aluminum leaching in magnesium salt-acetic acid compound system from ion-adsorption type rare earth ore [J]. Separation and Purification Technology, 2024, 334: 126070

[17] Wang G-f, Zhu J-x, Liang X-l, et al.. Industrial-scale sustainable rare earth mining enabled by electrokinetics [J]. Nature Sustainability, 2025, 8(2): 182-189

[18] Wang G-f, Xu J, Ran L-y, et al.. A green and efficient technology to recover rare earth elements from weathering crusts [J]. Nature Sustainability, 2023, 6(1): 81-92

[19] Yang L-f, Wang D-s, Li C-c, et al.. Searching for a high efficiency and environmental benign reagent to leach ion-adsorption rare earths based on the zeta potential of clay particles [J]. Green Chemistry, 2018, 20(19): 4528-4536

[20] Zhang Y-b, Zhang B-y, Yang S-q, et al.. Enhancing the leaching effect of an ion-absorbed rare earth ore by ameliorating the seepage effect with sodium dodecyl sulfate surfactant [J]. International Journal of Mining Science and Technology, 2021, 31(6): 995-1002

[21] Li J-f, Xiao Y-f, Feng X-j, et al.. Leaching of ion adsorption rare earths and the role of bioleaching in the process: A review [J]. Journal of Cleaner Production, 2024, 468: 143067

[22] Owusu-Fordjour E Y, Yang X-bo. Bioleaching of rare earth elements challenges and opportunities: A critical review [J]. Journal of Environmental Chemical Engineering, 2023, 11(5): 110413

[23] Wang M-y, Li J-n, Liu H-c, et al.. Rare earth element extraction from ionic rare earth ores by two typical acidogenic microorganisms, aspergillus Niger and acidithiobacillus ferrooxidans [J]. International Journal of Molecular Sciences, 2025, 26(5): 1986

[24] Zhao M-f, Zhang H-l, Han H-x, et al.. Differential leaching mechanisms and ecological impact of organic acids on ion-adsorption type rare earth ores [J]. Separation and Purification Technology, 2025, 362: 131701

[25] Wang L, Liao C-f, Yang Y-m, et al.. Effects of organic acids on the leaching process of ion-adsorption type rare earth ore [J]. Journal of Rare Earths, 2017, 35(12): 1233-1238

[26] Yang M-j, Liang X-l, Ma L-y, et al.. Adsorption of REEs on kaolinite and halloysite: A link to the REE distribution on clays in the weathering crust of granite [J]. Chemical Geology, 2019, 525: 210-217

[27] Miranda-Trevino J C, Coles C A. Kaolinite properties, structure and influence of metal retention on pH [J]. Applied Clay Science, 2003, 23(1–4): 133-139

[28] Bretti C, Cataldo S, Gianguzza A, et al.. Thermodynamics of proton binding of halloysite nanotubes [J]. The Journal of Physical Chemistry C, 2016, 120(14): 7849-7859

[29] Nguyen P M, Do P T, Pham Y B, et al.. Roles, mechanism of action, and potential applications of sulfur-oxidizing bacteria for environmental bioremediation [J]. Science of the Total Environment, 2022, 852: 158203

[30] Cama J, Ganor J. The effects of organic acids on the dissolution of silicate minerals: A case study of oxalate catalysis of kaolinite dissolution [J]. Geochimica et Cosmochimica Acta, 2006, 70(9): 2191-2209

[31] Wieland E, Stumm W. Dissolution kinetics of kaolinite in acidic aqueous solutions at 25°C [J]. Geochimica et Cosmochimica Acta, 1992, 56(9): 3339-3355

[32] Zhou H, Wang J-j, Yu X-y, et al.. Effective extraction of rare earth elements from ion-adsorption type rare earth ore by three bioleaching methods [J]. Separation and Purification Technology, 2024, 330: 125305

[33] Zhao Y, Zhao H-b, Shen L, et al.. Study on the role of microbial metabolites in in-situ noncontact bioleaching of ion-adsorption rare earth ore [J]. Journal of Environmental Management, 2024, 368: 122184

[34] Meng X-y, Zhao H-b, Zhao Y, et al.. Effective recovery of rare earth from (bio)leaching solution through precipitation of rare earth-citrate complex [J]. Water Research, 2023, 233: 119752

[35] Melo A, Quintelas C, Ferreira E C, et al.. The role of extracellular polymeric substances in micropollutant removal [J]. Frontiers in Chemical Engineering, 2022, 4: 778469

[36] Fu L-j, Fan D-k, Zhang J, et al.. Microstructure and properties of halloysite nanotubes and modification methods: A comprehensive review [J]. Applied Clay Science, 2024, 253: 107348

[37] Varga G. The structure of kaolinite and metakaolinite [J]. Epitoanyag - Journal of Silicate Based and Composite Materials, 2007, 59(1): 6-9

[38] Qiu S, Yan H-s, Qiu X-h, et al.. Adsorption of La on kaolinite (0 0 1) surface in aqueous system: A combined simulation with an experimental verification [J]. Journal of Molecular Liquids, 2022, 347: 117956

[39] Li Z, Bai T-s, Dai L-t, et al.. A study of organic acid production in contrasts between two phosphate solubilizing fungi: Penicillium oxalicum and Aspergillus Niger [J]. Scientific Reports, 2016, 6: 25313

[40] Zabiszak M, Nowak M, Taras-Goslinska K, et al.. Carboxyl groups of citric acid in the process of complex formation with bivalent and trivalent metal ions in biological systems [J]. Journal of Inorganic Biochemistry, 2018, 182: 37-47

[41] Cama J, Metz V, Ganor J. The effect of pH and temperature on kaolinite dissolution rate under acidic conditions [J]. Geochimica et Cosmochimica Acta, 2002, 66(22): 3913-3926

[42] Sung W, Inoue K I, Nihonyanagi S, et al.. Unified picture of vibrational relaxation of OH stretch at the air/water interface [J]. Nature Communications, 2024, 15(1): 1258

[43] Jordanov B, Tsankov D, Korte E H. Peculiarities in the stretching vibrations of the methylene groups [J]. Journal of Molecular Structure, 2003, 651–653: 101-107

[44] Upton D J, McQueen-Mason S J, Wood A J. An accurate description of Aspergillus Niger organic acid batch fermentation through dynamic metabolic modelling [J]. Biotechnology for Biofuels, 2017, 10(1): 258

[45] Wang T, Tian Z-m, Tunlid A, et al.. Nitrogen acquisition from mineral-associated proteins by an ectomycorrhizal fungus [J]. New Phytologist, 2020, 228(2): 697-711

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