Microbial bioleaching of rare earth elements from phosphate minerals: a biotechnology-driven systematic review of mechanisms, bioprocess determinants, and opportunities for sustainable recovery

Abstract

Abstract Background Rising demand for rare earth elements (REEs) and the severe environmental impact of conventional extraction from phosphate minerals (monazite, apatite) have intensified the search for green alternatives. Microbial bioleaching offers a low-energy, low-waste, and a sustainable biotechnological alternative by exploiting the ability of fungi and bacteria to generate organic acids, siderophores, reducing agents, and other metabolites that solubilize REEs. Although interest in REE bioleaching has increased, a biotechnology-focused synthesis of microbial mechanisms, metabolic constraints, and process determinants specific to phosphate matrices remains limited. Methods A PRISMA-guided systematic review was conducted. Scopus, Web of Science, PubMed, and Google Scholar and other major databases were searched to identify peer-reviewed studies reporting microbial bioleaching of REEs from phosphate minerals. From 443 identified records, 25 studies met the inclusion criteria after screening and eligibility assessment. These studies were evaluated based on microbial species, metabolic mechanisms, culture conditions, mineral substrates, and REE solubilization performance. Results Fungal species, particularly Aspergillus , Penicillium and Paecilomyces demonstrated the highest REE mobilization efficiencies through intensive production of citric, oxalic, and gluconic acids, along with phosphatase activity. Bacterial strains, including Acidithiobacillus , Bacillus , Pantoea , Burkholderia , Pseudomonas , and Klebsiella contributed complementary mechanisms such as proton extrusion, siderophore secretion, and Fe(III) / Fe(II) redox cycling. Bioleaching performance was strongly influenced by media composition, carbon source, nitrogen assimilation, pH evolution, mineralogy of the phosphate substrate, pulp density, and particle size. Across studies, the lack of standardized conditions limited direct comparability, but organic acid dominated pathways consistently produced the most robust REE solubilization. Conclusions Microbial bioleaching is a promising biotechnological platform for REE recovery from phosphate minerals, driven by metabolically diverse acidogenic, chelating, enzymatic, and redox mechanisms. However, advancements remain constrained by heterogeneous methodologies, limited integration of mechanistic studies, and minimal use of engineered strains or controlled bioreactor systems. Future progress requires standardized experimental frameworks, improved mechanistic understanding of organism-specific roles, and rational design of optimized microbial systems. This review offers a biotechnology-centered foundation to guide next-generation research on sustainable REE mobilization from phosphate resources.

Key findings

• ▸Microorganisms such as fungi and bacteria can generate organic acids, siderophores, and reducing agents to solubilize rare earth elements
• ▸Phosphate minerals like monazite and apatite can be targeted for bioleaching
• ▸Optimization of bioprocess conditions, such as pH, temperature, and nutrient supply, is crucial for efficient REE recovery

Keywords

Identifiers

DOI

10.1186/s12896-026-01125-1

Journal

BMC Biotechnology

Year

2026