Biomining at the Nexus of Microbial Ecology, Genomic Innovation, and Sustainable Resource Recovery

Biomining is an emerging biotechnological strategy that employs microorganisms to extract metals from ores and industrial wastes. Its growing importance is driven by climate-related environmental concerns, including habitat degradation, mine effluent pollution, fragility of global metal supply chains, and the increasing demand for critical metals essential to clean and low-carbon technologies. Although conventional mining has historically underpinned human civilization and technological progress, it is associated with significant ecological damage and resource inefficiency. Despite its promise, bio mining faces key constraints such as prolonged processing times, suboptimal metal recovery efficiencies, and limited selectivity, which have restricted large-scale commercial adoption. Most earlier reviews have primarily emphasized microbial metabolism and bioleaching pathways, with limited integration of sustainability metrics, process optimization strategies, and emerging applications such as electronic-waste valorization and nanoparticle recovery. The present review addresses these lacunae by providing a comprehensive and updated synthesis of biomining and bioleaching concepts, underlying mechanisms, and the role of environmental and soil-derived iron- and sulfur-oxidizing microorganisms. It further examines biomining applications in waste management, metal nanoparticle generation, and the use of genomic and omics-based tools for strain improvement and process control. Critical technological parameters influencing biomining performance, including particle size, pH selection, redox potential, temperature, aeration rate, solid concentration, microbial acclimatization, organic supplementation, and catalytic enhancement, are systematically analyzed. In addition, the review discusses major biotechnological approaches encompassing bacterial, fungal, and cyanidation-assisted biomining, with emphasis on industrial implementation and scalability. By integrating mechanistic insights with genomic advances and sustainability perspectives, this review offers an application-oriented framework to enhance biomining efficiency, scalability, and industrial relevance in the context of climate change and critical metal scarcity. Major Findings: This review identifies biomining as a sustainable alternative to conventional mining, driven by iron- and sulfur-oxidizing microorganisms. It highlights genomics-based process optimization, waste valorization, and control of critical operational parameters as key strategies to enhance metal recovery efficiency, scalability, and environmental sustainability.