Biological Mining: How Biotechnology Is Reshaping Mineral Processing

The Critical Minerals Problem

Every electric vehicle, wind turbine, and grid-scale battery requires copper, nickel, cobalt, and rare earth elements. Demand for these metals is growing faster than the industry can supply them. Meanwhile, ore grades are falling, new mine permits take 15+ years to obtain, and conventional mining accounts for an estimated 4–7% of global greenhouse gas emissions.

Conventional processing — blasting, crushing, smelting — consumes enormous energy and generates vast quantities of toxic waste. Miners need a better toolkit.

Biomining uses microorganisms, plants, and proteins to extract and recover minerals at a fraction of the energy cost and environmental footprint of traditional methods. It has been practiced at industrial scale since the 1980s and now accounts for roughly 20% of global copper production. A new generation of startups is extending its reach into nickel, rare earths, and mine waste recovery — backed by Rio Tinto, BHP, Vale, and Lowercarbon Capital.

The Biology: Four Approaches

Bioleaching deploys acid-tolerant bacteria — primarily Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans — that oxidize ferrous iron (Fe²⁺) to ferric iron (Fe³⁺). The ferric iron attacks sulfide minerals and releases the metals inside. The bacteria regenerate the oxidizing agent continuously, creating a self-sustaining extraction cycle. Heap leach operations apply this process at scale: crushed ore is stacked in engineered piles, irrigated with acidic solution, and left for bacteria to work through.

Biohydrometallurgy applies biological systems across the full hydrometallurgical chain, from ore dissolution through to final metal purification.

Phytomining uses hyperaccumulator plants — species that concentrate metals in their above-ground tissue at levels toxic to most organisms. Farmers harvest the biomass and processors extract the metal. The plants work soil that conventional mining cannot touch economically.

Biosorption uses biological materials (proteins, cell walls, engineered organisms) to selectively bind metal ions from dilute solutions, including mine wastewater and tailings pond water.

Endolith: AI-Guided Microbes for Copper Heap Leach

Endolith combines microbiology and machine learning to recover copper from ore grades that conventional processing cannot treat economically. The company’s platform pairs microbial consortia with continuous site monitoring and AI-guided adaptation: the microbes adjust their behavior based on real-time ore body data, improving recovery rates and cycle times with each deployment.

The technology integrates into existing heap-leach infrastructure without retrofits. BHP validated Endolith through its Think & Act Differently (TAD) program; field-scale deployments are now advancing across the Americas.

Copper demand is climbing from electrification, data center construction, and defense procurement. Most remaining reserves sit in low-grade ores that conventional smelting cannot treat at a profit. Endolith’s microbes access that stranded copper.

Allonnia: Proteins and Microbes Across the Mining Value Chain

Allonnia is a bio-ingenuity company spun out of Ginkgo Bioworks. Its two mining products address different points in the processing chain.

Allonnia D-Solve™ uses proprietary microorganisms to dissolve magnesium-bearing silicates (MgO minerals) in nickel, copper, and lithium ore. MgO causes grade penalties and cuts metal recovery in nickel sulfide circuits. At Lundin Mining’s Eagle Mine, D-Solve reduced MgO levels by up to 40% in pilot testing — enough to improve concentrate grades and lower smelter penalties. The product bolts onto existing processing circuits with no new infrastructure required.

Allonnia RE-Cover™ uses engineered proteins rather than whole organisms to capture and purify rare earth elements (REEs) from mine-impacted water and processing streams. Conventional REE separation relies on solvent extraction with large volumes of hazardous chemical waste. RE-Cover replaces that chemistry with selective protein binding, recovering REEs from dilute aqueous streams at a fraction of the waste burden.

Allonnia’s mining partners include Rio Tinto, BHP, Vale, and Mining3. In December 2025, the company closed a Series A extension of more than $20 million to accelerate deployments. Its 2040 targets: eliminate 200 million tonnes of mining waste and treat 600 billion gallons of contaminated water.

Genomines: Plants That Mine Nickel From Contaminated Soil

Genomines was founded in 2021 by mining engineer Fabien Koutchekian and plant biotechnologist Dr. Dali Rashid. The company uses synthetic biology to enhance nickel hyperaccumulator plants, then processes the harvested biomass to produce battery-grade nickel sulfate.

The process runs in four stages. First, Genomines engineers hyperaccumulator plant varieties to extract more nickel per hectare than wild-type species. Second, agronomists identify target soils: mine tailings and agricultural land with nickel concentrations too low or too dilute for conventional extraction. Third, the team plants and harvests the crop within months, optimizing growth through microbiome management and minimal fertilizer inputs. Fourth, processors convert the biomass into nickel precursors using bioleaching and downstream refining aimed at carbon neutrality.

The soil remediation benefit runs in parallel: hyperaccumulator crops pull toxic nickel out of contaminated land, leaving it suitable for agriculture or ecological restoration. Landowners get cleaned soil; Genomines gets the metal.

The IEA projects a 19x increase in nickel demand by 2040, driven by EV battery production. Genomines received a €5 million grant under France’s France2030 program and backing from Lowercarbon Capital. The World Economic Forum named it a top innovator in its Sustainable Mining Challenge.

The Broader Biomining Ecosystem

Allonnia, Endolith, and Genomines sit within a larger shift in how the industry approaches processing.

Several companies now develop biological replacements for toxic flotation chemicals and leaching reagents, cutting the chemical footprint of conventional circuits. Passive and active biological systems treat acid mine drainage and recover metals from process water in retrofitted operations. Engineered proteins and whole-cell biosensors bind specific metal ions with selectivity that solvent extraction chemistry cannot match, bypassing energy-intensive pyrometallurgy. Bioleaching researchers are also applying the technology to e-waste, spent batteries, and industrial residues, recovering critical metals from secondary streams and reducing pressure on primary mining.

BHP, Rio Tinto, Vale, Glencore, and Anglo American all run active biological processing programs. The research-to-commercial pipeline is moving.

The Economic and Environmental Case

Bioleaching and phytomining run at ambient temperature and pressure. Roasters, autoclaves, and smelters do not. That difference translates directly into lower energy costs and lower carbon emissions per tonne of metal produced.

Heap bioleach facilities cost a fraction of equivalent smelter capacity to build. Products like D-Solve integrate into existing circuits, so miners avoid greenfield construction costs.

As miners exhaust high-grade deposits, billions of tonnes of sub-economic ore and mine waste become treatable through biological processing. Tailings dams and waste rock dumps already contain substantial residual metal values; biological systems recover them while reducing long-term site liability.

Biological systems also reduce reliance on cyanide, sulfuric acid, and solvent extraction reagents. For operations in water-stressed or environmentally sensitive jurisdictions, that reduction matters to permit holders and regulators.

Challenges

Microbial systems are sensitive to temperature, pH swings, and complex ore body geochemistry. Heap bioleaching is slower than smelting for many ore types. Phytomining requires arable land and agronomic management that conventional miners do not have in-house. Regulators in many jurisdictions apply strict controls to open-field deployment of genetically modified organisms.

Scaling from laboratory pilot to industrial operation remains the hardest step. Many cleantech companies have collapsed in that gap. The validation partnerships that Endolith, Allonnia, and Genomines have secured with major mining groups are the clearest signal that their technologies have crossed the credibility threshold — these companies do not run public programs with unproven technology.

Falling ore grades, tighter environmental standards, and growing critical mineral demand are pushing miners toward biological solutions. The scaling challenge is an engineering and regulatory problem, not a scientific one.