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Biomining
Biomining
Biomining
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Biomining refers to any process that uses living organisms to extract metals from ores and other solid materials. Typically these processes involve prokaryotes, however fungi and plants (phytoextraction also known as phytomining) may also be used.[1] Biomining is one of several applications within biohydrometallurgy with applications in ore refinement, precious metal recovery, and bioremediation.[2] The largest application currently being used is the treatment of mining waste containing iron, copper, zinc, and gold allowing for salvation of any discarded minerals. It may also be useful in maximizing the yields of increasingly low grade ore deposits.[3] Biomining has been proposed as a relatively environmentally friendly alternative and/or supplementation to traditional mining.[2] Current methods of biomining are modified leach mining processes.[4] These aptly named bioleaching processes most commonly includes the inoculation of extracted rock with bacteria and acidic solution, with the leachate salvaged and processed for the metals of value.[4] Biomining has many applications outside of metal recovery, most notably is bioremediation which has already been used to clean up coastlines after oil spills.[5] There are also many promising future applications, like space biomining, fungal bioleaching and biomining with hybrid biomaterials.[6][7][8]

History of biomining

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The possibility of using microorganisms in biomining applications was realized after the 1951 paper by Kenneth Temple and Arthur Colmer.[9] In the paper the authors presented evidence that the bacteria Acidithiobacillus ferrooxidans (basonym Thiobacillus ferrooxidans) is an iron oxidizer that thrive in iron, copper and magnesium-rich environments.[9] In the experiment, A. ferrooxidans was inoculated into media containing between 2,000 and 26,000 ppm ferrous iron, finding that the bacteria grew faster and were more motile in the high iron concentrations.[9] The byproducts of the bacterial growth caused the media to turn very acidic, in which the microorganisms still thrived.[10] Following this experiment, the potential to use fungi to leach metals from their environment[11] and use microorganisms to take up radioactive elements like uranium and thorium[12] have also been explored.[11]

While the 1960s was when industrial biomining got its start, humans have been unknowingly using biomining practices for hundreds of years.[13] In western Europe the practice of extracting copper from metallic iron by placing it into drainage streams, used to be considered an act of alchemy.[13] However, today we know that it is a fairly simple chemical reaction.[13]

Cu2+ + Fe0 → Cu0 + Fe2+

In the Middle Ages in Portugal, Spain and Wales, miners unknowingly used this reaction to their advantage when they discovered that when flooding deep mine shafts for a period with some leftover iron they were able to obtain copper.[14]

In China, the use of biomining techniques has been documented as early as 6th-7th century BC.[15] The relationship between water and ore to produce copper was well documented, and during the Tang dynasty and Song dynasty copper was produced using hydrometallurgical techniques.[15] Though the mechanism of oxidation via bacteria was not understood, the unintended use of biomining allowed copper production in China to reach 1000 Tons per year.[15]

Current methods

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See also: Bioleaching

Biooxidation (biological pre-treatment)

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Biological pre-treatment utilizes the natural oxidation abilities of microorganisms to remove unwanted minerals that interfere with the extraction of the target metals.[16] This is not always necessary but is widely used in the removal of arsenopyrite and pyrite from gold (Au).[16] Adidithiobacillus spp. release the gold by the following reaction.[17]

2 FeAsS[Au] + 7 O2 + 2 H2O + H2SO4 → Fe2(SO4)3 + 2 H3AsO4 + [Au]

Stirred tank bioreactors are used for the biooxidation of gold.[16] While stirred tanks have been used to bioleach cobalt for copper mine tailings,[18] these are costly systems that can reach sizes of >1300m3 meaning that they are almost exclusively used for very high value minerals like gold.[16]

Illustration of the process of uranium heap leaching. In bioleaching, the heap would have been inoculated with the process specific microbe.

Bioleaching (bioprocessing)

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Dump bioleaching

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Dump Bioleaching was one of the first widely used applications of biomining. In dump bioleaching, waste rock is piled into mounds (>100m tall) and saturated with sulfuric acid to encourage mineral oxidation from native bacteria.[16] Inoculation of the rock with bacteria is often not performed in dump bioleaching which instead relies on the bacteria already present in the rock.[16]

Heap bioleaching

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Heap bioleaching is a newer take on dump leaching.[16] The process includes more processing in which the rocks are ground into a finer grain size.[16] This finer grain is then stacked only 2 – 10 m high and is well irrigated allowing for plenty of oxygen and carbon dioxide to reach the bacteria.[16] The mounds are also often inoculated with bacteria.[16] The liquid coming out at the bottom of the pile, called leachate, is rich in the processed mineral. The heaps reside on large non-porous platforms which are used to catch the leachate for processing.[16] Once collected the leachate is transported to a precipitation plant where the metal is reprecipitated and purified. The waste liquid, now void of the valuable minerals, can be pumped back to the top of the pile and the cycle is repeated.[16]

The temperature inside the leach dump often rises spontaneously as a result of microbial activities.[16] Thus, thermophilic iron-oxidizing chemolithotrophs such as thermophilic Acidithiobacillus species and Leptospirillum and at even higher temperatures the thermoacidophilic archaeon Sulfolobus (Metallosphaera sedula) may become important in the leaching process above 40 °C.[16]

In situ copper biomining of and electro-winning for recovery from Kupferschiefer deposits

In situ biomining

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In situ biomining involves the flooding and inoculation of fractured ore bodies that have yet to be removed from the ground.[16] Once the bacteria are introduced to the ore deposits, they begin leaching the precious metals, which can then be extracted as leachate with a recovery well.[19] In-situ mining also shows promise for applications in cost-effective deep subsurface extraction of metals.[20]

In situ biomining, is the one current method utilizing bioleaching that serves as an effective and viable replacement for traditional mining.[21] Because in-situ biomining, negates the need for the extraction of the ore bodies, this method stops the need for any hauling or smelting of the ore.[20] This would mean there would be no waste rocks or mineral tailings that contaminate the surface.[20] However, in-situ biomining also has the most environmental concerns of all of the leaching methods, as there is the potential for the contamination of ground water.[20][21] These concerns however can be careful managed, especially because most of this mining would occur below the water table.[20]

This method was used in Canada in the 1970s to extract additional uranium out of exploited mines.[22] Similarly to copper, Acidithiobacillus ferrooxidans can oxidize U4+ to U6+ with O2 as electron acceptor. However, it is likely that the uranium leaching process depends more on the chemical oxidation of uranium by Fe3+, with At. ferrooxidans contributing mainly through the reoxidation of Fe2+ to Fe3+.

UO2 + Fe(SO4)3 → UO2SO4 + 2 FeSO4

Applications

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A simplified scheme illustrating how to obtain copper by using bioleaching of chalcopyrite

One of the largest applications of these leaching methods is in the mining of copper Acidithiobacillus ferrooxidans has the ability to solubilize copper by oxidizing the reduced form of iron (Fe2+) with sulfur electrons and carbon dioxide.[23] This process results in ferric ions (Fe3+) and H+ in a series of cyclical reactions.

CuFeS2+4H++O2 --> Cu2++Fe2++2S0+2H2O,

4Fe2++4H++O2 4Fe3++2H2O,

2S0+3O2+2H2O→2SO2−4+4H+,

CuFeS2+4Fe3+→Cu2++2S0+5Fe2+,

The copper metal is then recovered by using scrap iron:

Fe0 + Cu2+ → Cu0 + Fe2+

Using bacteria such as A. ferrooxidans to leach copper from mine tailings has improved recovery rates and reduced operating costs. Moreover, it permits extraction from low grade ores – an important consideration in the face of the depletion of high grade ores.[3]

Economic feasibility and potential drawbacks

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It has been well established that bioleaching allows of the cheaper processing of low-grade ore when the bacteria are given the correct growth conditions.[24] This allows for economic extraction of low-grade ore and increases mining reserves in a sustainable way.[24]

Like any process of mineral recovery there are concerns about the ability to scale biomining to the size the industry would need. The biggest potential drawbacks of biomining are the relatively slow leaching and extraction times and need for expensive specialized equipment.[14] Biomining techniques only show economic viability as a complementary process to mining, not as a replacement. Biomining may make traditional mining more environmentally and economically friendly, by re-processing fresh or abandoned mine tailings and the detoxification of copper production concentrates to generate economically valuable copper-enriched liquors.[24] There is great economic feasibility for in-situ biomining to replace traditional mining in a cheaper and more environmentally friendly way, however it has yet to be adopted on any large scale.[14]

Gold

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Gold is frequently found in nature associated with arsenopyrite and pyrite. In the microbial leaching process Acidithiobacillus ferrooxidans etc. dissolve the iron minerals, exposing trapped gold (Au):[25]

2 FeAsS[Au] + 7 O2 + 2 H2O + H2SO4 → Fe(SO4)3 + 2 H3AsO4 + [Au]

Biohydrometallurgy is an emerging trend in biomining in which commercial mining plants operate continuously stirred tank reactor (STR) and the airlift reactor (ALR) or pneumatic reactor (PR) of the Pachuca type to extract the low concentration mineral resources efficiently.[3]

The development of industrial mineral processing using microorganisms has been established in South Africa, Brazil and Australia. Iron-and sulfur-oxidizing microorganisms are used to release copper, gold, and uranium from minerals. Electrons are pulled off of sulfur metal through oxidation and then put onto iron, producing reducing equivalents in the cell in the process. This is shown in this figure.[26] These reducing equivalents then go on to produce adenosine triphosphate in the cell through the electron transport chain. Most industrial plants for biooxidation of gold-bearing concentrates have been operated at 40 °C with mixed cultures of mesophilic bacteria of the genera Acidithiobacillus or Leptospirillum ferrooxidans.[27] In other studies the iron-reducing archaea Pyrococcus furiosus were shown to produce hydrogen gas which can then be used as fuel.[28] Using Bacteria such as Acidithiobacillus ferrooxidans to leach copper from mine tailings has improved recovery rates and reduced operating costs. Moreover, it permits extraction from low grade ores – an important consideration in the face of the depletion of high grade ores.

The acidophilic archaea Sulfolobus metallicus and Metallosphaera sedula can tolerate up to 4% of copper and have been exploited for mineral biomining. Between 40 and 60% copper extraction was achieved in primary reactors and more than 90% extraction in secondary reactors with overall residence times of about 6 days. All of these microbes are gaining energy by oxidizing these metals. Oxidation means increasing the number of bonds between an atom to oxygen. Microbes will oxidize sulfur. The resulting electrons will reduce iron, releasing energy that can be used by the cell.

Bioremediation

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Bioremediation is the process of using microbial systems to restore the environment to a healthy state by detoxifying and degrading environmental contaminants.[29]

When dealing with mine waste and metal toxic contamination of the environment, bioremediation can be used to lessen the mobility of the metals through the ecosystem.[30] Common mine and metal wastes include arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc which can make its way into the environment through rain and waterways where it can be moved long distances.[30] These metals pose potential toxicology risks to wild animals and plates as well as humans.[30] When the right microbes are introduced to mines or areas with mining contamination and toxicity, they can alter the structure of the metals to make it less bioavailable and lessening its mobility in the ecosystem.[30] It is important to note however, that certain microbes may increase the amount of metals that get dissolved into the environment.[30] This is why scientific studies and testing must be conducted to find the most beneficial bacteria for the situation.[30]

Image from the shorelines affected by the Exxon Valdez oil spill of 1998

Bioremediation is not specific to metals. In 1989 an Exxon Valdez oil tanker spilled 42 million liters of crude oil into Prince William Sound.[5] The oil was washed ashore by tides and covered 778 km of the shoreline of the sound, but also spread to covered 1309 km of the gulf of Alaska.[5] In attempts to rejuvenate the coast after the oil spill, Exxon and the EPA began testing bioremediation strategies, which were later implemented on the coast line.[5] They introduced fertilizer to the environment that promoted the growth of naturally occurring hydrocarbon degrading microorganisms.[5] After the applications, microbial assemblages were determined to be made up of 40% oil degrading bacteria, and one year later that number had fallen back to its baseline of around 1%.[5] Two years after the spill, the region of contaminated shoreline spanned 10.2 km.[5] This case indicated that microbial bioremediation may work as a modern technique for restoring natural systems by removing toxins from the environment.

Future prospects

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Additional capabilities, of current bioleaching technologies include the bioleaching of metals from sulfide ores, phosphate ores, and concentrating of metals from solution.[4] One project recently under investigation is the use of biological methods for the reduction of sulfur in coal-cleaning applications.[31]

Biomining in space

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Theoretical map of space biomining/bioleaching based biological life support system (BLSS)

The concept of space biomining is creating a new field in the world of space exploration.[6] The main space agencies believe that space biomining may provided an approach to the extraction of metals, minerals, nutrients, water, oxygen and volatiles from extraterrestrial regolith.[32][33][6] Bioleaching in space also shows promise for application in building biological life support systems (BLSS).[6] BLSS do not usually contain biological component, however, the use of microorganisms to breakdown waste and regolith, while being able to capture their byproducts like nitrates and methane would theoretically allow for a cyclical system of regenerative life support.[6]

Fungi in biomining

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Species of filamentous fungi, specifically those in the genera of Aspergillus and Penicillium have been shown as effective bioleaching agents.[7] Fungi have the ability to solubilize metals through acidolysis, redoxolysis and chelation reactions.[7] Like bacteria, fungi have been studied for their ability to extract rare earth elements and to process low grade ore. But their most promising and studied usage is in the breakdown of E-waste and the recovery of valuable metals from it, like gold.[7][34] Despite the promise of fungal bioleaching, there has been no industrial applications of it as it does not out compete its bacterial counterparts.[7]

Hybrid biomaterials

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Hybrid Biomaterials are created by attaching peptides to magnetic nanoparticles.[8] The peptides attached are specific proteins that have the capacity to bind to organic/inorganic materials with high affinity.[8] This allows for highly specific custom hybrid molecules to be developed, that bind to molecules of interest.[8] The magnetic nanoparticles that these proteins are bound to, allow for the separation of the biomaterial and the bound molecules from an aqueous solution.[8] There has already been successful development of these hybrid biomaterials for eluting gold and molybdenite from solution, and this technique shows great promise for cleaning up tailing ponds.[8]

See also

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References

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Biomining

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Biomining is a biotechnological process that utilizes acidophilic microorganisms to extract valuable metals from low-grade ores, mineral concentrates, and waste materials through mechanisms such as and biooxidation, providing an alternative to traditional pyrometallurgical methods. The technique involves the microbial oxidation of minerals, where and like Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans, and Sulfolobus metallicus generate ferric iron and to solubilize metals such as , , , and . In , insoluble metal s are converted directly into soluble sulfates, enabling metal recovery from solutions, while biooxidation pretreats refractory ores by removing sulfur and iron layers that encase precious metals like in . These processes typically occur in acidic environments ( 1.0–2.0) and can operate at temperatures ranging from ambient to 85°C, often in heap, dump, or tank reactors. Historically, biomining traces its roots to ancient practices at sites like the Rio Tinto mine in , where microbial activity inadvertently aided silver and as early as pre-Roman times, but commercial biohydrometallurgy only emerged in the mid-20th century with the identification of key acidophiles in the and large-scale implementation in the 1970s. As of 2025, it accounts for more than 20% of global production—primarily through in —and 5% of recovery, particularly for refractory ores, with additional applications in , , and extraction from low-grade sources and e-waste. Compared to conventional , biomining offers significant advantages, including lower energy consumption, reduced emissions of and other pollutants, higher extraction efficiencies (>90% for some metals), and the ability to process ores with grades as low as 0.5% metal content that are uneconomical by . It also facilitates metal recovery from mine tailings and industrial wastes, minimizing environmental contamination and promoting resource recycling. Recent advancements focus on engineering acidophiles via to enhance tolerance to metal toxicity, high temperatures, and osmotic stress, as well as using microbial consortia for improved in complex polymetallic ores.

Fundamentals

Definition and Principles

Biomining is defined as the extraction of metals using microorganisms to facilitate the solubilization of valuable elements from low-grade ores, mine wastes, and via biohydrometallurgical processes. These processes harness the metabolic activities of acidophilic microbes to target minerals, converting insoluble metal sulfides into soluble forms that can be recovered downstream. The core principles of biomining revolve around microbial oxidation of minerals to liberate associated metals, coupled with the production of acids and oxidizing agents that promote metal solubilization through complexation. Acidophilic microorganisms oxidize reduced and iron compounds, generating ferric iron (Fe³⁺) as a potent oxidant and to maintain the acidic environment essential for leaching. For instance, iron oxidation proceeds via the reaction \ceFe2+−>Fe3++e−\ce{Fe^{2+} -> Fe^{3+} + e^{-}}, primarily mediated by Acidithiobacillus species, while oxidation yields according to \ceS+1.5O2+H2O−>H2SO4\ce{S + 1.5 O_2 + H_2O -> H_2SO_4}. These reactions enable the breakdown of lattices, releasing metals like and into aqueous solutions. A fundamental distinction in biomining mechanisms is between direct and indirect action: in direct mechanisms, microorganisms physically attach to mineral surfaces and enzymatically oxidize the sulfides, whereas indirect mechanisms involve the production of lixiviants—such as Fe³⁺ and H₂SO₄—in the bulk solution, which chemically attack the without requiring cell-mineral contact. Biohydrometallurgy, as a primary of biomining, emphasizes these biological pathways and operates with low energy input at ambient or mildly elevated temperatures, contrasting sharply with the high-temperature requirements of pyrometallurgical .

Microorganisms Involved

Biomining primarily relies on acidophilic prokaryotes that oxidize iron and sulfur compounds to facilitate metal solubilization from ores. Among these, Acidithiobacillus ferrooxidans is a key mesophilic bacterium, thriving at optimal 1.5–2.5 and temperatures of 20–40°C, where it oxidizes ferrous iron (Fe²⁺) to ferric iron (Fe³⁺) and elemental to . This Gram-negative, autotrophic chemolithotroph derives energy from the oxidation of reduced inorganic compounds while fixing (CO₂) via the Calvin-Benson-Bassham cycle. Its adaptations to extreme acidity and high metal concentrations include efflux pumps, such as those encoded by the ars operon for arsenic resistance, and mechanisms that sequester toxic ions on the cell surface. Another prominent primary prokaryote is Leptospirillum ferriphilum, an extreme (optimal ~1.8, ~37°C) that specializes in iron oxidation, contributing to the regeneration of the ferric iron oxidant essential for . Lacking sulfur-oxidizing capabilities, it complements sulfur-oxidizers in microbial communities and exhibits robust tolerance to , including up to 30 g/L , through enhanced efflux systems and metabolic adjustments. Secondary microbes extend biomining to higher temperatures. Sulfobacillus thermosulfidooxidans, a moderate (optimal 1.9–2.4, up to 60°C), oxidizes both iron and , supporting processes in warmer environments. Similarly, the archaeon Sulfolobus metallicus functions as a hyper (optimal ~2.0, 70–80°C), oxidizing and iron in extreme heat, which is advantageous for ores. Fungal contributors, such as and Penicillium simplicissimum, play a role in at near-neutral through heterotrophic metabolism, producing organic acids like citric and via and the tricarboxylic acid (TCA) cycle to chelate metals. These fungi operate effectively at pH 3–6, offering alternatives for less acidic conditions, though their application in biomining remains more exploratory compared to prokaryotes. The metabolic foundation of these prokaryotes is autotrophic chemolithotrophy, where is harvested from the exergonic oxidation of Fe²⁺ (via electron transport chains involving and rusticyanin) and (through :quinone oxidoreductase and other enzymes), coupled with CO₂ fixation for synthesis. Tolerance to toxic metals is mediated by active efflux pumps (e.g., resistance-nodulation-division transporters) that expel ions like and mercury, alongside passive onto extracellular polymeric substances. In practice, synergistic microbial consortia outperform pure cultures; for instance, mixed communities of A. ferrooxidans with Leptospirillum spp. or heterotrophs like Acidiphilium enhance iron and oxidation rates, accelerating by improving acid production and mineral attachment, with reported efficiency gains in dissolution.

Historical Development

Early Observations

Early observations of biomining phenomena date back to ancient civilizations, where unintentional metal extraction occurred through natural processes involving acidic drainage waters. The earliest documented instances of processes akin to biomining in date to the (960–1279 AD), where wet production via microbial leaching in drainage waters yielded up to 1,000 tons per year to support state coinage needs. Similarly, in medieval , silver-copper mines, such as those in the Iberian Belt, produced acidic runoffs that naturally dissolved metals from ores through oxidation, contributing to inadvertent leaching long before scientific recognition. In the 19th and early 20th centuries, miners noted "sour liquors"—highly acidic solutions—in tailings from sulfide ore processing, which accelerated metal dissolution beyond expected chemical rates. A prominent example is the Rio Tinto mines in Spain, where intensive pyrite extraction since the mid-19th century generated drainage with pH as low as 1–2 due to natural and mining-induced pyrite oxidation, releasing iron, copper, and other metals into waterways. These observations highlighted the role of acidic environments in mineral breakdown but were initially attributed solely to abiotic reactions. Scientific identification of microbial involvement began in the mid-20th century. In 1947, researchers reported the presence of in (AMD) from coal mines, demonstrating their contribution to production and iron solubilization. This was advanced in 1951 by the discovery of the iron-oxidizing bacterium Thiobacillus ferrooxidans (now classified as Acidithiobacillus ferrooxidans) in coal mine drainage waters, where it catalyzed the autotrophic oxidation of ferrous iron to ferric iron under acidic conditions, accelerating AMD formation. By the 1960s, laboratory experiments confirmed that microorganisms like Acidithiobacillus ferrooxidans significantly enhanced the release of metals from sulfide minerals, with dissolution rates 10 to 100 times faster than abiotic processes alone, laying the groundwork for intentional biomining applications.

Modern Commercialization

The commercialization of biomining accelerated in the 1970s with pioneering pilot-scale bioleaching operations for copper recovery from low-grade sulfide ores. At the Bingham Canyon Mine in Utah, USA, Kennecott Copper Corporation initiated early commercial bacterial leaching in the late 1950s, but expanded efforts in the 1970s demonstrated practical recoveries of 20-30% metals from waste dumps using naturally occurring acidophilic bacteria such as Acidithiobacillus ferrooxidans. The 1980s and 1990s marked widespread industrial adoption, particularly for heap bioleaching of and biooxidation of refractory ores. In , the Quebrada Blanca mine commissioned a fully bioleaching-based operation in 1994, processing heaps of 100,000 to 500,000 tons of mixed oxide- ores and producing over 80,000 tons of annually by the mid-2000s. For , Gencor launched the world's first commercial biooxidation plant at the Fairview Mine in in 1986, treating refractory concentrates to liberate encapsulated particles through bacterial oxidation. By the 2000s, biomining had achieved global scale, contributing approximately 20% of the world's production, with major operations at sites like the Escondida mine in , which integrated for secondary ores. Tank-based biooxidation for also expanded, as exemplified by the Ashanti Goldfields Company's Sansu plant in , commissioned in 1994 and scaled to reactors exceeding 1,300 m³ by the early 2000s, enabling treatment of over 790 tons of concentrate per day. Key innovations included Mintek's development of the BIOX® process in during the , a patented bacterial oxidation method for refractory that facilitated multiple commercial plants worldwide. Complementing this, BacTech advanced moderately thermophilic bacterial oxidation technologies in the , achieving over 90% oxidation in pilot and full-scale recovery operations, such as at the Youanmi mine in . In the , biomining increasingly integrated with hydrometallurgical processes like solvent extraction and , enhancing overall efficiency and achieving recovery rates up to 90% in optimized and operations, as seen in expanded Chilean heap systems and advanced BIOX® facilities. In the 2020s, biomining continued to expand, with Quebrada Blanca Phase 2 achieving initial production in 2023 and ramping up, contributing to bioleaching's share of approximately 20% of global copper production as of 2025.

Biomining Techniques

Biooxidation

Biooxidation serves as a critical pretreatment method in biomining for ores, where valuable metals such as are encapsulated within matrices that resist conventional extraction techniques. The process involves the aerobic microbial oxidation of these minerals, primarily (FeS₂) and (FeAsS), converting them into soluble sulfates and thereby liberating the entrapped metals for subsequent recovery, often via cyanidation. This biological approach employs acidophilic to catalyze the oxidation, producing ferric ions (Fe³⁺) that chemically attack the sulfide structure, enhancing metal accessibility without the high energy demands of pyrometallurgical alternatives. Operationally, biooxidation is performed in a series of agitated tank s, with commercial-scale volumes reaching up to 1,500 m³ per to handle substantial throughputs. The process typically maintains a retention time of 4-6 days at temperatures of 30-40°C and a low range of 1.5-2.0 to optimize microbial activity. Oxygen sparging is essential, as it supports the bacterial oxidation of ferrous iron (Fe²⁺) to ferric iron (Fe³⁺), which drives the breakdown of minerals; air or pure oxygen is introduced to achieve dissolved oxygen levels sufficient for efficient reaction kinetics. Key microorganisms involved include species like Acidithiobacillus ferrooxidans, which thrive under these acidic, aerobic conditions. The fundamental chemistry of pyrite biooxidation can be represented by the following equation: 4FeS2+15O2+2H2O→2Fe2(SO4)3+2H2SO44\text{FeS}_2 + 15\text{O}_2 + 2\text{H}_2\text{O} \rightarrow 2\text{Fe}_2(\text{SO}_4)_3 + 2\text{H}_2\text{SO}_4 This reaction illustrates the complete aerobic oxidation to soluble iron(III) sulfate and sulfuric acid, facilitated by microbial regeneration of the oxidant. Biooxidation offers distinct advantages for processing sulfide refractory ores, often containing 10-30% sulfides, achieving up to 95% sulfide oxidation and enabling effective pretreatment where direct leaching fails. It is particularly suited for ores rich in gold, uranium, and nickel, providing a cost-effective, lower-emission alternative to roasting by minimizing SO₂ emissions and energy use. Notable commercial implementations include the BIOX® process, which has treated refractory gold concentrates to yield recovery rates up to 90% post-cyanidation, and the ASTER™ process, which integrates biooxidation for similar high-efficiency sulfide destruction in gold extraction.

Dump and Heap Leaching

Dump and heap leaching represent scalable, low-cost biomining methods for extracting metals, particularly , from low-grade s by percolating acidic solutions through large piles, facilitated by acidophilic microorganisms that oxidize minerals. In dump leaching, the process utilizes existing waste rock dumps, often exceeding 100 m in height and containing low-grade with less than 0.5% metal content, where dilute (pH 1.5–2.5) is irrigated at rates of 5–10 L/m²/h to promote microbial activity and metal solubilization. This method is inherently slow, typically requiring years to achieve recoveries of 50–70%, due to the heterogeneous nature of the uncrushed material and limited control over environmental variables. Heap leaching, in contrast, involves purpose-built engineered stacks of ore, typically 3–10 m high, with the material crushed to less than 10 mm to enhance permeability and microbial access, placed on lined impermeable bases for efficient collection of the pregnant leach solution (PLS). is facilitated through embedded pipes to supply oxygen, supporting microbial oxidation, while irrigation with acidified maintains optimal conditions; the process is faster, often completing in months with recoveries of 70–90%. Key parameters include temperature gradients from ambient to 50°C, which influence microbial consortia, and initial inoculation with acidophiles like Acidithiobacillus species to accelerate startup. Unlike dumps, which repurpose waste with minimal preparation, heaps are actively constructed for optimized flow and recovery. The overall process flow begins with the introduction of acidified water and air to the pile, enabling microbial oxidation of sulfides to produce ferric ions that solubilize metals, resulting in PLS containing dissolved metals such as Cu²⁺, which is then processed via solvent extraction and to recover pure metal. For (CuFeS₂), the primary , microbial oxidation follows the simplified reaction under acidic conditions: CuFeS2+4O2+2H+→Cu2++Fe2++2SO42−\text{CuFeS}_2 + 4\text{O}_2 + 2\text{H}^+ \rightarrow \text{Cu}^{2+} + \text{Fe}^{2+} + 2\text{SO}_4^{2-} This step generates ferrous iron, which bacteria reoxidize to ferric for continued leaching. Notable examples include the large-scale heaps at Chuquicamata in Chile, covering over 1 km², where bioleaching of low-grade sulfides has produced significant copper output, demonstrating the commercial viability of these surface-based techniques.

In Situ Biomining

In situ biomining represents an innovative underground extraction technique that solubilizes metals directly within ore deposits without the need for excavation, relying on microbial catalysis to target sulfide minerals in deep or inaccessible formations. The process begins with the injection of oxygenated, acidic lixiviant solutions—typically sulfuric acid-based with dissolved oxygen and ferric iron—into the ore body, often through flooded underground mine workings or fractured strata. Acidophilic microorganisms, such as those from the Acidithiobacillus genus, colonize the subsurface environment and oxidize the sulfides, liberating metals into a soluble form as part of the pregnant leach solution (PLS). This PLS is subsequently pumped to the surface via recovery wells for further processing and metal precipitation. Ongoing pilots, such as the EU's BIOMOre project at Rudna mine in Poland (2015-2020) and subsequent studies as of 2023, continue to test indirect bioleaching at depths up to 1 km. Technical implementation requires strategic borehole drilling to enhance ore permeabilization through hydraulic fracturing or natural fissure exploitation, ensuring efficient lixiviant distribution. Injection occurs at controlled flow rates of 5-20 L/min per well, maintaining a highly acidic below 2 and temperatures of 20-50°C to optimize microbial activity and reaction rates; these conditions are often achieved naturally via the exothermic oxidation process, with recirculation of regenerated ferric iron from surface bioreactors. The general microbial-mediated dissolution of metal sulfides follows the adapted reaction: MS+2O2+2H+→M2++SO42−+H2O\text{MS} + 2\text{O}_2 + 2\text{H}^+ \rightarrow \text{M}^{2+} + \text{SO}_4^{2-} + \text{H}_2\text{O} where MS denotes the metal sulfide and the process generates sulfuric acid in situ, sustaining the low pH. Recovery involves pumping the PLS to surface solvent extraction and electrowinning plants, where metals are stripped and purified. One key advantage of in situ biomining is its reduced surface footprint, avoiding large-scale earthmoving and infrastructure typical of conventional mining, which minimizes ecosystem disruption and land rehabilitation needs. Capital costs are substantially lower than those for open-pit operations due to eliminated excavation and milling requirements, making it viable for deep-seated or low-grade deposits that are otherwise uneconomic. For instance, conceptual and pilot applications target deep copper sulfides, such as in Poland's Rudna mine, where the method suits uneconomic remnants below 1 km depth. Despite these benefits, biomining is constrained by slow leaching kinetics, often requiring 1-5 years for substantial metal mobilization due to limited subsurface flow and microbial colonization rates. poses a significant risk, as acidic, metal-bearing leachates could migrate beyond the zone if permeability barriers fail, necessitating robust monitoring and containment strategies. To date, the approach remains largely at the pilot scale, highlighting scalability hurdles for broader commercialization.

Applications in Metal Recovery

Base Metals Extraction

Biomining plays a dominant role in the extraction of base metals, particularly , where it accounts for approximately 15% of global production. This process is especially effective for low-grade ores containing 0.4-0.6% , which are uneconomical for traditional . Through , microorganisms such as Acidithiobacillus ferrooxidans oxidize sulfide minerals, producing and ferric iron that facilitate the dissolution of into soluble (CuSO₄). Recovery efficiencies in these operations typically reach 80-90%, enabling the processing of vast volumes that would otherwise be discarded. A prominent example is the mine in , the world's largest producer, which has utilized since the 1990s to recover over 500,000 tons of annually from low-grade oxide and sulfide ores. At Bingham Canyon in the , contributes to the mine's total output of around 300,000 tons of per year (as of 2025), supporting approximately 25% of production through enhancement of extraction-electrowinning (SX-EW) processes for secondary minerals. The Talvivaara mine in (now operated as Terrafame since 2017 following environmental challenges and ) demonstrates integrated - biomining, where bioheap leaching recovers alongside primary targets from polymetallic black schist ores, despite past controversies involving groundwater contamination. These operations integrate biomining with downstream to produce high-purity cathode . Nickel extraction via biomining targets both and ores, with biooxidation achieving recovery rates of 70-85% through heap or tank leaching methods. For laterites, hybrid processes like followed by enhance accessibility of by partial sulfation before microbial oxidation. The Talvivaara operation exemplifies this, yielding about 70% recovery after 13-14 months of primary heap , with co-recovery of at lower rates due to associations. These approaches are particularly viable for low-grade deposits, integrating with or for metal refinement. Other base metals, such as and , benefit from biomining in pilot and commercial scales. Zinc recovery from ores reaches up to 70% in pilots, leveraging acidophilic to oxidize zinc sulfides in stirred-tank or heap configurations. For , of sulfide-rich achieves extractions of around 90%, as demonstrated in mini-pilot studies using iron- and sulfur-oxidizing consortia. These processes often recover multiple metals simultaneously and culminate in for pure metal production, offering a sustainable alternative to . Biomining for base metals provides notable environmental advantages, including a reduction in smelting-related emissions by up to 50% through avoidance of high-temperature processes and lower energy demands. At sites like , this translates to decreased SO₂ releases and minimized waste generation compared to conventional methods.

Precious Metals Recovery

Biomining plays a crucial role in recovering precious metals, particularly and silver, from refractory ores where the metals are encapsulated within minerals such as and . Approximately 60-70% of global reserves are , requiring pretreatment to liberate the for subsequent extraction via cyanidation. Biooxidation processes oxidize these matrices, exposing the precious metals and enabling high recovery rates, typically achieving 90-95% during cyanidation following treatment. For gold recovery, established biooxidation methods like the BIOX® process utilize acidophilic bacteria to break down refractory sulfides in agitated tanks, followed by conventional cyanidation. The Albion Process™ complements this by combining ultrafine grinding with atmospheric oxidative leaching, further enhancing liberation of encapsulated gold particles. These techniques are particularly effective for low-grade ores containing less than 1 g/t Au, making economic extraction viable where traditional methods fail. Silver is often co-extracted alongside copper or gold, with bioleaching targeting minerals like acanthite (Ag₂S) in heap operations, yielding 60-80% recovery rates. The integrated biomining workflow for precious metals typically involves and oxidation to pretreat the , followed by leaching to dissolve the liberated metals and carbon adsorption to recover them from solution. Notable commercial examples include the São Bento mine in , operational from 1991 to 2013, which produced up to 100,000 ounces of annually using BIOX® pretreatment on refractory sulfide . Similarly, Newmont's Carlin operations in the USA implemented heap biooxidation for whole- treatment starting in 2000, processing Carlin Trend refractory deposits to achieve viable recovery. These processes also reduce consumption by up to 30% compared to direct cyanidation of untreated refractory , minimizing environmental risks while improving overall efficiency. In some sandstone-hosted deposits, biomining facilitates co-recovery of alongside precious metals, with achieving approximately 70% recovery in Wyoming's roll-front deposits through microbial oxidation of and reduction zones. This approach leverages acid-tolerant to enhance in or heap configurations, supporting multifaceted metal extraction from complex geological settings.

Rare Earth Elements and E-Waste

Biomining has emerged as a promising method for recovering rare earth elements (REEs) from secondary sources such as mine tailings and , leveraging acidophilic like Acidithiobacillus ferrooxidans to solubilize metals including (Nd) and (La). In a two-step process using co-cultures of A. ferrooxidans and Acidiphilium cryptum, recoveries reached 70.7% for Nd and 84.5% for La from , demonstrating enhanced solubilization through biological acid production and jarosite formation. Similarly, single-step with A. ferrooxidans from phosphate rock achieved 32.5% recovery for Nd and 37.0% for La under optimized conditions of pH 2 and 1% pulp density. These microbial processes reduce reliance on external chemical acids compared to traditional , promoting lower environmental impact through in situ acid generation via oxidation. In e-waste recycling, biomining targets printed circuit boards (PCBs) to extract REEs alongside precious metals like (Au), palladium (Pd), and copper (Cu), using fungi such as to produce organic acids like citric and for metal solubilization. with A. niger and mixed cultures has yielded up to 100% Cu recovery and 48% Au recovery from PCBs over 28-30 days, while REE recoveries, including cerium (Ce), europium (Eu), and yttrium (Y), reached 80-99% in optimized fungal and bacterial systems. Processes adapted for , such as variants inspired by commercial technologies like BioX, enable selective recovery from complex e-waste matrices without high-energy . Biomining is also applied in in-situ resource utilization (ISRU) for recovering rare earth elements and other metals from extraterrestrial regolith on bodies like the Moon and Mars. Fungi such as Penicillium simplicissimum produce organic acids to leach metals from regolith simulants, while bacteria like Acidithiobacillus ferrooxidans facilitate extraction through iron and sulfur oxidation. Experiments, including the BioRock project on the International Space Station, have demonstrated efficient recovery of rare earth elements from basalt simulants under microgravity and simulated Martian gravity conditions, with no significant reduction in performance compared to Earth-based tests. Furthermore, Acidithiobacillus ferrivorans and related species contribute to detoxifying perchlorates in Martian regolith simulants via electrotrophic reduction, achieving removal rates of approximately 19 mg/L per day under acidic conditions, thereby mitigating toxicity for potential human exploration. These processes support broader ISRU goals, including oxygen production through integrated microbial systems like photosynthetic cyanobacteria. Key mechanisms in REE biomining include , where microbial cell surfaces bind REE ions, and , involving intracellular uptake facilitated by specialized proteins like lanmodulin (LanM) in methylotrophic . LanM exhibits picomolar affinity for lanthanides, enabling selective binding and separation of REEs from mixed solutions with high specificity. For instance, (LLNL) research in 2024 utilized engineered LanM proteins for biosorption from coal byproducts, achieving high selectivity for light REEs in low-grade feedstocks like coal fly ash. These approaches offer advantages in handling heterogeneous waste matrices, recovering critical REEs such as essential for magnets and , while minimizing toxic outputs compared to pyrometallurgical methods. Projections indicate that biomining could contribute significantly to REE supply diversification by , potentially meeting a growing share of demand amid geopolitical supply constraints. A notable case is the EU-funded (2022-2025), which concluded in having developed protocols for REE extraction from e-waste, integrating microbial consortia to achieve scalable urban mining with reduced chemical inputs and demonstrating improved recovery efficiencies in pilot tests.

Economic and Environmental Considerations

Economic Feasibility

Biomining exhibits a favorable cost structure compared to traditional and pyrometallurgical methods, primarily due to its reliance on microbial processes that eliminate the need for high-temperature furnaces and extensive infrastructure. Capital expenditures (CAPEX) for commercial-scale biomining operations typically range from USD 100-500 million for large-scale heap or setups, representing a substantial reduction—often 30-60% or more—of the costs associated with equivalent pyrometallurgical facilities. Operating expenditures (OPEX) for biomining, such as heap or dump leaching, are estimated at USD 0.5-2 per kg of recovered, lower than the USD 3-6 per kg for pyrometallurgical processing of low-grade ores, enhancing viability for uneconomical deposits. Revenue generation in biomining is driven by its applicability to low-grade ores containing less than 0.5% metal content, achieving recovery rates of 60-88% through processes, which extends the economic life of deposits otherwise unviable for traditional extraction. Payback periods for biomining projects are typically 1-5 years, supported by steady metal output and lower ongoing costs once operational. The global biomining market, valued at USD 2.1 billion in , is estimated at USD 2.3 billion in , reflecting growing adoption for sustainable metal recovery amid depleting high-grade reserves. In , U.S. policy reports emphasize investing in biomining for domestic critical supply, potentially boosting market growth. In comparisons to conventional methods, biomining offers savings of up to 30%, consuming around 250 kWh per of processed without the high-heat roasting required in . Water usage is also reduced, at approximately 0.3 s per of in heap , about 50% less than typical hydrometallurgical processes, enhancing (ROI) particularly for remote or water-scarce sites where costs are prohibitive. Economic viability of biomining is influenced by ore , with ores particularly suited due to microbial affinity, optimal scales exceeding 1 million tons of ore per year for heap operations, and sensitivity to metal prices—such as exceeding USD 3 per pound to ensure profitability. A notable case is the Talvivaara mine in , with total investments exceeding €1 billion (approximately USD 1.1 billion) and targeting 50,000 tons of production annually, but it filed for in 2014 due to environmental overruns, production shortfalls, and fluctuating prices.

Challenges and Drawbacks

One of the primary technical challenges in biomining is the slow kinetics of the process, which typically requires weeks to months for metal extraction, in contrast to the days or hours needed for pyrometallurgical methods. This delay arises from the biological nature of microbial oxidation, where acidophilic like Acidithiobacillus ferrooxidans gradually oxidize minerals, limiting throughput in industrial operations. Another key issue is passivation, where iron precipitates such as jarosite form layers that block mineral pores and hinder microbial access, particularly in leaching. To mitigate passivation, the addition of chloride ions has been shown to enhance dissolution rates by preventing sulfur layer formation and catalyzing copper release, though concentrations must be carefully controlled to avoid microbial . Biomining microorganisms are also highly sensitive to variations in temperature and , with optimal ranges typically between 30–45°C and 1.5–2.5; deviations can inhibit growth and reduce efficiency. Environmental risks associated with biomining include the potential generation of when leachates are unmanaged, leading to soil and water acidification. Re-processing of mine through biomining can mobilize like and , exacerbating leakage into surrounding ecosystems if containment fails. Mitigation strategies involve using impermeable liners in heap setups to prevent and adding lime for neutralization of acidic effluents, which raises and precipitates metals for safer disposal. Operationally, heap and dump leaching in biomining are weather-dependent, as excessive rainfall can dilute the acidic lixiviant and slow microbial activity, while arid conditions may limit . High salinity levels exceeding 50 g/L, often from or , inhibit microbial growth by disrupting cell membranes and enzyme function in most acidophiles, though halotolerant strains like Acidihalobacter prosperus offer partial adaptation. Biomining generally poses lower health and safety risks than traditional due to reduced need for explosives and heavy machinery, but biohazards from extremophilic microbes, such as aerosolized Acidithiobacillus species, require protective measures like protocols. Scalability remains limited for complex, low-grade ores containing multiple sulfides, as microbial consortia struggle with inhibitory impurities, necessitating pre-treatment or strain optimization. To address these hurdles, brief applications of genetic engineering have enhanced strain robustness; for instance, CRISPR-Cas9 editing of Acidithiobacillus ferridurans improves tolerance to metals and chloride, boosting leaching efficiency. Closed-loop systems, which recycle process water and minimize evaporation, can significantly reduce overall water loss, promoting sustainability in water-scarce regions.

Bioremediation Applications

Biomining microbes, particularly sulfate-reducing bacteria (SRB) such as Desulfovibrio species, play a key role in remediating mine waste by precipitating heavy metals as insoluble sulfides in acid mine drainage (AMD), which typically has a pH of 3-5. These bacteria reduce sulfate to sulfide under anaerobic conditions, enabling the removal of metals like zinc and copper with efficiencies ranging from 80% to over 95% in laboratory and field settings. For instance, Desulfovibrio strains tolerate metal concentrations up to 100 mg/L while maintaining high sulfate reduction rates, facilitating in situ precipitation without extensive chemical inputs. In tailings treatment, processes recover residual metals from mining wastes while stabilizing the material through microbial activity, reducing environmental mobility. At the Berkeley Pit in , —an abandoned copper mine site flooded since the 1990s—pilot-scale applications of bacterial sulfate reduction have demonstrated ongoing microbial neutralization of acidic waters laden with metals like iron and . These efforts integrate SRB to promote , mitigating generation and enabling partial metal recovery as a secondary benefit. Beyond mining contexts, microbes similar to those in biomining contribute to oil spill cleanup through biosurfactant production, which enhances emulsification and for degradation. Pseudomonas species produce rhamnolipids, that disperse oil into microdroplets, accelerating microbial breakdown. In the 1989 Exxon Valdez spill, which released approximately 42 million liters of crude oil into Alaska's , efforts incorporating such biosurfactants aided in achieving up to 70% of spilled hydrocarbons within the first year, as nutrients and boosted indigenous microbial populations. Additional applications include e-waste detoxification via fungal biosorption, where metal-accumulating fungi bind like and iron from electronic scraps. Fungi such as Pleurotus florida exhibit high capacities, removing over 95% of (up to 97 mg/g) through binding and enzymatic activity, offering a low-energy method to detoxify leachates from discarded devices. Similarly, in leverages dissimilatory metal-reducing bacteria at sites like the Old Rifle facility in , where 2000s pilot tests injected electron donors like to stimulate U(VI) reduction to immobile U(IV), lowering soluble concentrations from 5 μM to below 1 μM over months. These strategies are inherently and cost-effective, with operational costs for microbial metal removal estimated at $1-5 per kg compared to over $10 per kg for conventional chemical precipitation methods, while simultaneously integrating with environmental stabilization.

Future Directions

Sustainability Enhancements

Recent advances in biomining technologies during the have focused on minimizing and water demands, with processes demonstrating lower energy consumption than conventional pyrometallurgical methods by eliminating the need for energy-intensive roasting steps. Closed-circuit systems further enhance by recycling approximately 80-85% of process water, reducing reliance on freshwater sources and mitigating risks of in arid regions. Emissions from biomining are notably lower than traditional methods that rely on . Additionally, certain acidophilic microbes employed in these processes facilitate CO₂ fixation, enabling carbon-neutral operations by converting atmospheric CO₂ into and carbonates during metal oxidation. In support of principles, biomining enables the reprocessing of mine tailings to recover residual metals such as , , , and , transforming waste into valuable resources and reducing the environmental burden of legacy sites. Regulatory frameworks have increasingly favored biomining through standards like the Initiative for Responsible Mining Assurance (IRMA) , which emphasizes low-impact extraction methods including biological processes to meet environmental and social benchmarks set by the and UN. For instance, Mintek's green initiatives in leverage microbial oxidation to avoid release during processing, offering substantial reductions in SO₂ emissions compared to . Life-cycle assessments (LCAs) of biomining operations reveal lower than pyrometallurgical alternatives, primarily due to reduced energy inputs and emissions. Integration with sources, such as solar-heated heaps to maintain optimal microbial activity temperatures, further lowers the and enhances overall in remote operations. As of 2025, pilot projects integrating biomining with have shown promise in supplying critical metals for technologies.

Emerging Innovations

Recent advancements in biomining are pushing the boundaries of microbial applications beyond traditional terrestrial ore processing, incorporating fungi, extraterrestrial environments, engineered biomaterials, genetic modifications, and computational optimizations to enhance efficiency and expand resource recovery. Fungi offer promising alternatives for leaching metals from e-waste and neutral ores through the production of s such as citric and oxalic acids, which solubilize metals without requiring extreme acidity. For instance, has been utilized in rare earth elements (REEs) from , where mechanisms including control, , and enable effective extraction under milder conditions compared to bacterial methods. In a 2024 study, this fungus achieved substantial REE recovery from phosphor-containing waste, demonstrating up to 80-90% solubilization of key elements like and after optimization of culture conditions. These fungal approaches are particularly suited for scenarios, where low-grade, neutral-pH materials predominate. Biomining concepts are extending to extraterrestrial resource utilization, with and ESA exploring microbial extraction from lunar and Martian to support in-situ resource utilization for future missions. Acidithiobacillus species, known for iron and sulfur oxidation on , have been tested in microgravity on the , successfully extracting iron and aluminum from regolith simulants by forming biofilms that enhance mineral dissolution despite reduced sedimentation. These experiments simulate Mars gravity conditions and indicate that biomining could yield essential metals like Fe and Al for habitat construction. As of November 2025, with Artemis II delayed to 2026, such innovations remain in conceptual and ISS testing phases, addressing the logistical challenges of transporting materials from toward potential self-sustaining colonies. Hybrid biomaterials are emerging as selective tools for REE recovery, leveraging engineered proteins like lanmodulin (LanM) for high-affinity binding. LanM, derived from methylotrophic bacteria, exhibits exceptional selectivity for REEs over competing ions, achieving binding efficiencies exceeding 95% in low-pH environments through its unique beta-hairpin structure that coordinates lanthanides. When immobilized on , LanM forms bio-nano hybrids that integrate microbial leaching with targeted adsorption, accelerating overall metal recovery by up to twofold compared to free microbial systems by enhancing and specificity. These hybrids show promise for processing complex ores or e-waste streams. Genetic engineering via CRISPR-Cas systems is tailoring microbes for harsher biomining conditions, such as elevated temperatures and metal toxicities. For example, CRISPR editing of Acidithiobacillus ferridurans has introduced genes mitigating toxic ion release while boosting tolerance to , allowing sustained activity in high-stress leachates. Engineered strains now exhibit optimal performance at 60°C, expanding applicability to refractory ores that require thermal pre-treatment, with projections of 50% efficiency improvements in leaching rates by 2030 through iterative refinements. Microbial consortia for enhanced biomining, particularly for of battery wastes, have shown improved performance. In , consortia recover up to 95% of and 96% of using acid-producing in multi-step processes, minimizing energy inputs while targeting specific metals. Such optimizations could revolutionize closed-loop recovery from electronic discards, aligning with goals.

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