Multi-Scale and Trans-Disciplinary Research and Technology Developments of Heap Bioleaching

Abstract

Heap bioleaching is considered to be a less energy-intensive metal-extraction technique compared to other methods, making it particularly attractive for low-grade sulfide ores. It has been successfully applied to recovery of copper, gold, and uranium from ores over decades. Despite its seemingly straightforward nature, heap bioleaching can experience failures if the ore is unsuitable or the heap leach process is not thoroughly investigated and well-developed. Therefore, multidisciplinary approaches are essential for research and development in heap bioleaching, as its performance depends on numerous processes operating across a wide range of length scales. This review focused on the current state of knowledge regarding the understanding of multi-scale mechanisms in heap bioleaching and the use of multidisciplinary approaches at different scales to develop the process. The investigation covered various scales, such as atomic and molecular, mineralogy and microbes, reaction particles, heap bioleaching units and full-scale factory production. Different approaches were employed to gain a comprehensive understanding of the microbial molecular structure and metabolism, the structure and reaction of minerals, microbial–mineral interaction, particles and aggregation states, and multiphase flow transfer, as well as laboratory experiments, modeling, industrialization, and operation optimization. We emphasized the need for collaboration among researchers from different disciplines and stress the importance of considering the coupling effects of physical, chemical, and microbiological factors when running heap bioleaching plants. Such collaboration and coupling are vital for successful implementation and optimization of heap bioleaching processes. This paper aimed to provide a comprehensive overview of current research related to heap bioleaching at different scales and disciplines, and gave implications to heap bioleaching technology development.

1. Introduction

High-grade metal ore resources are declining globally, leading to increased attention on low-grade sulfide ores [1]. Bioleaching technology has gained popularity in the mining industry for economically recovering important metals like copper, gold, and uranium. However, its contribution to overall metal production remains relatively small. Researchers are currently exploring the application of bioleaching in other ore types as well as in waste processing [2].

Heap bioleaching was inadvertently used in China and Europe hundreds of years ago, although the microorganisms involved were not recognized at that time [3]. In the last few decades, large-scale heap leaching was initially employed for treating oxidized uranium, gold, and silver ores. With the discovery of acidophilic iron- and sulfur-oxidizing microbes, heap leaching expanded to include the processing of sulfide ores [4]. Heap leaching first became prominent for gold recovery from low-grade ores using cyanide in the early 1970s [5]. Over time, it evolved into a key hydrometallurgical technology for copper recovery from both oxides and secondary sulfides, often coupled with solvent extraction and electrowinning processes [6]. Currently, heap leaching accounts for approximately 20% of global copper production [3], and has recently been explored for nickel, zinc, and uranium recoveries [7].

Compared to other extraction technologies, heap leaching is a cost-effective and time-efficient process that sometimes incorporates microorganisms to enhance leaching rates and reduce costs. Typically, heap bioleaching is conducted using ore sizes around P₈₀ = 10–25 mm after agglomeration, although larger sizes, including run-of-mine (ROM) size, can also be used [8]. In some cases, much smaller sizes of about P₈₀ = 5 mm are employed. Heap bioleaching involves both chemical and microbiological reactions occurring at the micro scale on the mineral surface, while the leaching process takes place in large heap piles that can span kilometers [9]. It exhibits characteristics across multiple levels and scales, ranging from atomic to kilometer scales. The mechanisms involved in heap bioleaching encompass various fields, such as microbiology, molecular biology, chemical engineering, biological engineering, metallurgical reaction engineering, mineral engineering, mining engineering, physical chemistry, heat transfer, and seepage mechanics [10,11,12]. Therefore, research on heap leaching requires collaboration among researchers from different disciplines, necessitating multi-scale investigation. Although heap bioleaching projects have been implemented worldwide, the heap bioleaching efficiency of each ore depends on a more comprehensive understanding of the fundamental processes underlying it on various fronts.

This paper aims to provide a comprehensive overview of current research related to heap bioleaching, spanning from atomic and molecular fundamentals to industrial-scale applications. It highlights the tools and challenges associated with optimizing heap bioleaching projects in an industrial setting. Due to its trans-disciplinary nature, successful research and development of heap bioleaching requires collaboration between experts from multiple fields. Innovative solutions are developed to address the challenges associated with heap bioleaching, optimize the process for maximum metal recovery, and minimize its environmental impact.

2. Mechanisms and Processes of Heap Bioleaching

2.1. Mechanisms of Sulfide Mineral Bio-Oxidation

The mechanisms of bioleaching have been extensively studied in recent decades [13,14,15,16]. The fundamental mechanism of heap bioleaching involves sulfide mineral dissolution in an acidic ferric solution assisted by microbial oxidation. It is generally understood that certain functional microbes assist in the re-oxidation of Fe²⁺ to Fe³⁺, which serves as the oxidant for leaching. Additionally, some microbes oxidize intermediate sulfur compounds, reducing the passivation layers and exposing fresh mineral surfaces for oxidation.

Earlier literature speculated about direct enzyme reactions of microbes on sulfide mineral surfaces, leading to the differentiation between “direct” and “indirect” bioleaching mechanisms [17,18]. However, the direct transfer of electrons via enzymes or nanowires between metal sulfides and attached cells has not been conclusively demonstrated, suggesting that a direct mechanism may not exist. Instead, researchers have proposed contact and non-contact leaching mechanisms [16,19]. According to this theory, the primary oxidant is Fe³⁺, regardless of the presence of microbes. Concentrated Fe³⁺ within the extracellular polymeric substances (EPS) significantly enhances the oxidation rate of sulfide minerals in the microbial activity space. This theory assumes that EPS can concentrate Fe³⁺ through organic compounds and elevate the redox potential in the microenvironment. However, recent research has shown the weak absorption ability of EPS for Fe³⁺, with even weaker absorption than Fe²⁺. This suggests no preferential absorption of Fe³⁺ in this area and no elevation of the redox potential in this micro environment [20]. This indicates that the mineral surface may primarily serve as a habitat for microbes, housing significantly more microbes than the planktonic microbes in the solution. The attached iron-oxidizing microbes, both attached and planktonic, play a role in re-oxidizing Fe²⁺ to Fe³⁺. Similarly, attached sulfur-oxidizing microbes contribute to the oxidation of intermediate sulfur compounds formed during sulfide mineral oxidation, which reduces passivation layers and increases the oxidation rate of sulfide ores.

Although ferric iron reacting with sulfide mineral surfaces remains the fundamental process in bioleaching, it does not diminish the importance of the microbial function. Microbes play a crucial role in regenerating ferric iron and eliminating intermediate sulfur compounds. Under acidic conditions, natural oxidation of Fe²⁺ to Fe³⁺ is extremely slow, while bacteria increase the oxidation rate by up to five orders of magnitude [21,22]. Elemental sulfur oxidation is also greatly enhanced by sulfur-oxidizing microbes [19]. The microbial method is considered the most cost-effective for regenerating ferric oxidants, as no additional materials need to be added to the system.

2.2. Heap Bioleaching Operation

While there are various methods available for recovering metals from ores, such as flotation, agitated tank leaching and vat leaching, heap leaching is often preferred due to its financial advantages. Heap leaching is a cost-effective technique, characterized by its short process and low investment and operational costs. However, it generally exhibits lower metal recovery rates compared to other methods, making it more suitable for treating low-grade ores. While copper, uranium, and gold ores are the primary targets for heap bioleaching, it is also being considered for zinc, cobalt, and nickel ores, as well as electronic waste [3,23,24,25].

Heap bioleaching involves stacking the ore as a heap on an impermeable pad and applying appropriate leaching reagents, such as acidified solutions for copper or cyanide solutions for gold ores, to the top of the heap [26]. Leaching occurs through the action of microorganisms residing within the ore bed and mineral oxidation facilitated by ferric ion (Fe³⁺) as the oxidant. It is commonly employed for the oxidizing leaching of copper sulfides and as a pretreatment method for refractory gold ores. Following leaching, metals in the pregnant leach solution (PLS) are directed to a PLS pond and recovered using different processes. Carbon absorption is typically used for cyanide-leached gold solutions, while solvent extraction and electrowinning are employed for recovering copper from acidic leachates. The “barren” leach solution is pumped to a barren solution pond, where it undergoes solution makeup before being reapplied to the surface of the heap [27].

Despite its widespread industrial use, heap bioleaching still faces challenges such as low recoveries, lengthy extraction times, and high operational costs [28]. Unlike other chemical or biological industrial processes, heap bioleaching is more complex and difficult to control. This complexity arises from the intricate reactions involving physical, chemical, and biological aspects, as well as the variations in ore composition, local climate, and microbiological conditions. Consequently, each heap bioleaching project requires careful study from the outset, with a focus on optimizing heap operations.

3. Multi Scales Related to Heap Bioleaching Process

Heap bioleaching exhibits characteristics across multiple levels and scales, and as research progresses, the understanding of these multi-level and multi-scale aspects becomes increasingly clearer. Like other chemical engineering processes [29], the heap bioleaching process involves in levels of atom/molecular, mineralogy/microbes, reaction particles, heap bioleaching units, factory, and meso-scale phenomena, and is more profound due to its large scale (Figure 1). While the research content and focus differ across these levels, in principle, technology, equipment and systems, each level gives rise to various sub-disciplines. These levels correspond to distinct phases of research and development in heap bioleaching, encompassing material innovation, reactor research and development, and system integration. Therefore, trans-disciplinary collaboration is essential for the successful development and industrialization of heap bioleaching on theoretical, experimental, and computational platforms. Mineralogists provide details of the leaching ore for microbiologists to select suitable microbes. Microbiologists optimize microbial communities for enhanced metal solubilization and bioleaching efficiency. Genomic and metagenomic experts analyze genetic information to identify key microbial species and metabolic pathways crucial for process optimization. Bioinformaticians monitor microbial dynamics and metabolic activities in heap leaching through advanced computational tools, providing real-time insights for adjusting operational parameters. Process engineers design and refine bioleaching processes, integrating biological insights to improve metal recovery rates and product quality, and recent AI and automation developments further elevate the efficiency. Environmentalists provide details of the environmental impact of the process. This interdisciplinary synergy ensures the continuous advancement and application of bioleaching technology.

3.1. Atom/Molecular

Different sulfide minerals exhibit varying crystal structures, which in turn influence their oxidation mechanisms and rates. Metal sulfides can be conductors, semiconductors, or insulators depending on the arrangement of metal and sulfur atoms in their crystal lattice [30]. These natural metal sulfides originate from geological or biological events, including pyrite (FeS₂), chalcopyrite (CuFeS₂), troilite (FeS), pyrrhotite (Fe₇S₈), hauerite (MnS₂), molybdenite (MoS₂), tungstenite (WS₂), galena (PbS), sphalerite (ZnS), orpiment (As₂S₃), and realgar (As₄S₄) et al.

According to molecular orbital and valence band theories, the orbitals of individual atoms or molecules form electron bands with different energy levels. Metal sulfides, such as FeS₂, MoS₂, and WS₂, consist of pairs of sulfur atoms forming nonbonding orbitals. As a result, the valence bands of these metal sulfides are derived solely from the orbitals of the metal atoms, making them resistant to proton attack and insoluble in acid. These sulfides can only be broken down through multistep electron transfers with an oxidant, such as iron (III) ions. On the other hand, the valence bands of some other metal sulfides, excluding the aforementioned three, arise from both metal and sulfur orbitals. Protons can remove electrons from these valence bands, resulting in cleavage of the bonds between the metal and sulfur components of the metal sulfide, making them relatively soluble in acid [16,31,32]. These sulfides, FeS₂, MoS₂, and WS₂, follow the thiosulfate mechanism, where Fe³⁺ attacks metal sulfides by extracting electrons and is subsequently reduced to Fe²⁺. Simultaneously, the metal sulfide minerals release metal cations and water-soluble intermediate sulfur compounds. On the other hand, the other sulfides follow the polysulfide pathway, leading to the formation of elemental sulfur on the reaction surface [16,17,32].

The microbial oxidation of iron and sulfur by acidophiles forms the basis for bioleaching of sulfide minerals. During this process, Fe³⁺ attacks metal sulfides by extracting electrons and is reduced to Fe²⁺. Additionally, intermediate sulfur compounds accumulate on the mineral surface, with elemental sulfur being particularly stable in acidic environments. Naturally occurring acidophiles that inhabit sulfide mineral environments have evolved the ability to oxidize iron (II) to iron (III) ions and sulfur compounds in acidic solutions, such as Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans, and Acidithiobacillus caldus. The catalytic activity of microbes significantly accelerates the oxidation of Fe (II) and elemental sulfur [21,22].

The microbial iron oxidation pathway involves electron transport pathways, the expression and regulation of the rus operon, and the use of electron transport carriers in both downhill and uphill processes. The sulfur oxidation pathway includes the oxidation of elemental sulfur and sulfites. In A. ferrooxidans, the sulfur oxidation enzyme system primarily consists of a sulfur dioxygenase and quinone oxidoreductase for sulfide oxidation, along with an oxidoreductase acceptor, thiosulfate thiotransferase, thiosulfate dehydrogenase, tetrathionate hydrolase, and adenosine 5’-phosphosulfate for sulfuric acid oxidation [33,34]. Electrons transported through energetically favorable pathways are reduced to H₂O in the downhill process and, in the uphill process, against the redox potential gradient, they reduce to NAD(P) (H) during the oxidation of Fe (II). The sulfur oxidation pathway of A. ferrooxidans involves relevant genes and operons, a mechanism for sulfur oxidation, and the sulfur oxidase system. The iron and sulfur oxidation pathways play a crucial role in the energy-acquisition process of autotrophic acidophiles.

3.2. Mineralogy/Microbial Consortium

The feasibility of heap leaching is determined by the type of ore associated with metal minerals. Direct heap leaching is employed for oxidized ores such as copper oxide and oxidized gold ores to recover the metals. However, for sulfide ores like copper sulfides and sulfide-bearing gold ores, bioleaching microbes are used in processing plants. While heap leaching has primarily been used in copper mines, it is now mainly applied to secondary copper minerals, resulting from oxidation of copper sulfide minerals, downward migration of soluble copper sulfates, and precipitation as copper sulfide by reaction with primary sulfide minerals, particularly chalcocite [14]. Chalcopyrite, the most abundant copper-containing mineral in the Earth’s crust, constitutes 70% of these minerals [3]. However, the bioleaching efficiency of chalcopyrite is currently insufficient for industrial-scale application [35,36,37].

Challenges can arise in heap leaching due to the presence of gangue minerals and clay minerals that consume acid. Acid consumption in ores is influenced by factors such as the existence of carbonates, short-term and long-term acid-consuming components, and the degree of acid adsorption by non-carbonate minerals like clays, hydrated iron oxides, highly porous copper minerals, and silts that form minerals [38]. Carbonates such as calcite exhibit high reactivity with acid and can dissolve even under much-diluted sulfuric acid conditions. Silicates like chlorite and epidote can significantly increase acid consumption during extended leaching periods. Silicates can have a more substantial impact on overall acid consumption than carbonates. Clay minerals such as montmorillonite, kaolinite, smectite, and mordenite are responsible for elevated acid consumption and reduced copper recoveries [39].

In addition to the mineral type, the distribution pattern of minerals within the ore plays a crucial role in heap leaching efficiency. Since heap leaching utilizes coarse ore particles, the exposure of minerals to the leaching solution is important. Some metal minerals are distributed in veins within the ore, and, when the ore fractures, it tends to crack more easily along areas where sulfide minerals are concentrated, facilitating the extraction of copper and other metals. Secondary copper sulfide ores, for example, form in clearances among gangue minerals after secondary mineralization, allowing for high leaching rates with coarse particles. However, many metal minerals, like chalcopyrite, are dispersed within gangue minerals and require finer particle sizes for complete exposure. Crushing the ore to a smaller particle size is often necessary to achieve full exposure of these minerals, highlighting the importance of reducing particle size in successful heap leaching operations.

Acidophilic autotrophic iron-oxidizing microbes such as A. ferrooxidans and L. ferrooxidans, as well as sulfur-oxidizing microbes like A. caldus and A. thiooxidans, play a crucial role in facilitating the leaching of sulfide minerals [40,41,42]. A comprehensive in silico study of over 100 representative complete and draft genomes of Acidithiobacillia members has been conducted, utilizing analyses of genome relatedness indexes, in silico DNA–DNA hybridization, phylogenomic reconstruction based on ribosomal proteins, and sets of conserved “core” proteins related to metabolic features [43]. Similar to mineralogy, the microbial communities present in different leaching heaps can vary; this highlights the progress in microbial characterization and the need for studies with an ecological approach in bioleaching processes. The composition of the microbial community composition is influenced by initial inoculation, ore characteristics, and the conditions of the heap leaching process [9,42,44].

3.3. Reaction Particles

Heap bioleaching is commonly performed on crushed and agglomerated ores with a top size of 12–25 mm, while larger particles may also be used in run-of-mine dump leaching. Microbial-assisted heap bioleaching involves the reaction between small units of ore particles, air, leachate containing sulfuric acid and iron, and functional microbes.

At the sulfide mineral scale, Fe³⁺ attacks the sulfide minerals on the mineral surface, releasing Fe²⁺ into the solution while generating intermediate sulfur compounds through thiosulfate and polysulfide pathways. This reaction and diffusion are assumed to follow the shrinking-core type model [12]. It is crucial to consider the availability of oxygen and trivalent iron during the mineral leaching process. The activity of the microbial community composition in the contact interface and solution, the redox potential of the mineral contact solution, the development of the surface passivation layer, the inward diffusion of oxidant trivalent iron, and the outward diffusion of metal ions are all critical factors. Microbes within the system can exist in suspended or adsorbed states. Suspended microbes primarily work to regenerate trivalent iron, while adsorbed microbes on the mineral surface serve to regenerate trivalent iron and decrease sulfur intermediates, thus alleviating the passivation effects during the reaction. The interaction between microbes and minerals significantly accelerates the oxidation process of the minerals [19].

At the ore particle scale, leaching is influenced by the distribution of mineral particles within a single particle, known as the topological effect. Mineral particles can range from being free to being encapsulated within other particles. The accessibility and distribution of these particles determines the extent of leaching for target minerals. The mineralogy of the gangue matrix plays a significant role in interfering with mineral leaching and biological phenomena, since gangue minerals account for the majority of the ore. Acid consumption minerals usually result in elevated pH levels and Fe³⁺ precipitation on the ore particles. This iron precipitation leads to the passivation of the surface of reaction particles results in insufficient oxidants, and affects reaction kinetics. Diffusion of gas and ion from the particle containing both sulfide minerals and gangue minerals is crucial for leaching. This diffusion process is governed by factors such as the diffusion gradient, diffusivity of species, ore particle size, and porosity.

3.4. Heap Leaching Units

Heap leaching is unique due to its relatively coarse particle size and the topological structure formed in heaps. In heap bioleaching, the flow and transport of gas and solution through the heaps is even more crucial than the reaction under single particles [45]. This is because the supply of oxidants and their contact with the particles forms the foundation for the ongoing leaching reaction. Although knowledge about the flow, transport, and reaction around a single particle, as well as the overall performance of the reactor, is possessed, understanding of what occurs at the meso-scale level of particle clusters (the second meso-scale) and how it influences multi-phase transfer and reaction remains limited.

Multi-phase transfer in heaps involves mechanisms such as advection, diffusion, dispersion, and convection in the solid phase, liquid phase, and gas phase [46], and has a significant impact on the overall efficiency and recovery of the process. Inadequate solution flow, for example, can result in incomplete leaching and poor metal recovery. Conversely, excessive gas flow may cause channeling and bypassing of the leach solution, leading to uneven leaching and decreased recovery rates. Additionally, multi-phase transfer influences the geochemical and physical properties of the ore heap, including pH, Eh, hydraulic conductivity, and porosity. These factors further affect leaching kinetics and the quality of the final product obtained from the process.

Modern heap leach facilities require contributions from various fields to ensure sustainable design and operation. These fields include hydrometallurgy, civil engineering, geotechnical engineering, unsaturated-flow hydrology, mine planning, geosynthetics engineering, geochemistry, process engineering, mechanical engineering, and electrical engineering. Despite advancements in these fields, challenges persist in the heap leaching industry. Failure of heap leaching often happened when scaling up, since the multi-phase transfer at heap leach scale is not easy simulated in laboratory tests, resulting in inaccurate scale-up assumptions, insufficient control of the geochemical environment within the heap, alterations in the mechanical and hydraulic properties of the ore, and ineffective solution management systems. Most heap leach operations experience poor or lower than expected metal recovery.

3.5. Factory

At the system level, considerable knowledge regarding the design and ecological impact of individual reactors is already possessed. However, our understanding of effectively integrating diverse reactors and processes to establish a circular economy with minimal detrimental ecological effects is still limited. When designing and operating a heap bioleaching plant, it is vital to consider factors such as overall metal recovery and comparability of different processes, as well as economic and environmental aspects.

The heap bioleaching process must align with the subsequent extraction process to ensure the stability and economy of the overall process. In the case of heap bioleaching, the leachate is then extracted and purified to obtain metals like copper and uranium (Figure 2). During the heap bioleaching process of copper sulfide ore, acid, iron, and impurity ions in the circulating solution continue to accumulate, making the subsequent extraction–electrowinning process more challenging. To reduce the burden of extraction–electrowinning, it is sometimes necessary to properly neutralize the leaching solution and remove some impurities. For instance, chlorination leaching in the heap bioleaching process of copper sulfide ore can significantly improve copper leaching efficiency but can have a negative impact on the subsequent extraction–electrowinning process. In the industrial operation of the Zijinshan copper mine, high acidity and high iron concentration were initially used in the leaching solution, resulting in high copper leaching rates but low solvent extraction efficiency [47]; then later, the leachate was neutralized to maintain a lower acidity and lower ionic concentration solution, enhancing the solvent extraction efficiency [48,49].

Similarly, oxidized residue generated from the peroxidation of primary sulfide gold ore can be used for gold extraction through methods like cyanidation or other extractants (Figure 2). However, it is important to note that producing elemental sulfur via the peroxidation of sulfide minerals leads to increased cyanide consumption. Additionally, the accumulation of ions in the leaching solution of uranium ore can cause issues such as scaling within the ion adsorption column during subsequent adsorption and extraction processes. Hence, when designing the overall process, factors like leaching efficiency, impurity output, purification efficiency, and others must be considered to ensure process compatibility, minimize environmental impact, and maximize economic benefits.

Heap bioleaching reduces the need for energy-intensive processes like grinding and smelting, thereby lowering greenhouse gas emissions and minimizing environmental impact [7]. Furthermore, it enables the extraction of metals from ores that would otherwise be economically unviable using conventional techniques. However, like any mining process, careful management is necessary to mitigate potential environmental risks, such as proper containment of leachate and measures to prevent groundwater contamination.

4. Methods and Tools for Heap Bioleaching Research at Different Scales

4.1. Microbiology and Molecular Biology

Microbial tools have been utilized to uncover the composition, structure, diversity, and ecological functions of microorganisms in bioleaching systems. Commonly employed methods for analyzing microbial communities include culture-based isolation, 16S rRNA sequencing, metagenomics, transcriptomics, proteomics, and single-cell sequencing et al. (

Table 1. Tools for research on bioleaching microbial community composition, function, and activity detection.

Tools	Function	References
Culture-based isolation	Species isolation under given condition	[50]
Total DNA amount	Microbial abundance detection	[51]
16S rRNA sequencing	Microbial community composition revealing	[52]
Q-PCR	Abundance of selected species	[53,54]
Geo Chips	Function genes identification	[55,56]
Metagenome	Whole genome of the species or community	[57,58]
Transcriptome	Complete set of RNA molecules	[59]
Proteome	Complete set of proteins	[60]
Single-cell sequencing	Analysis of genetic material from individual cells	[61]

).

Initially, bioleaching microorganisms were isolated as pure strains for physiological and functional research. Culture-based isolation allows for the direct isolation of cultivable microorganisms, enabling further investigation into their physiological and biochemical characteristics [50]. However, this approach captures only a fraction of the microbial community composition and does not provide a comprehensive understanding of all microbial information. There are still a significant number of bacteria that are difficult to culture and obtain in pure strains, necessitating the use of alternative research methods.

With the advent of culture-independent approaches utilizing PCR amplification, techniques such as denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments have been employed to analyze the microbial community composition present in bioleaching heaps [62]. Then, high-throughput sequencing has simplified 16S rRNA gene sequencing [43]. Quantitative PCR (Q-PCR) methods have also been used to determine the abundance of each species in the system. However, Q-PCR methods have limitations as they are limited to tested species and cannot provide a comprehensive representation of the entire microbial community composition.

To assess total microbial abundance in bioleaching systems, alternative methods have been explored, such as measuring total DNA extracted from heap-leached ore [51]. Marker genes have also been selected to evaluate aspects such as CO₂ and N₂ availability, osmotic stress response, ferrous iron oxidation, and sulfur oxidation activity in the bioleaching process [63]. GeoChip technology offers a high-throughput approach by using probes that target genes involved in metabolic pathways related to carbon and nitrogen cycling, metal resistance, and stress response. By analyzing environmental samples using the GeoChip, researchers can determine the presence of specific genes within the microbial community composition and gain insight into its functional potential. Studies utilizing the GeoChip method have revealed stronger microbial community composition abilities on ore surfaces compared to those in solution [55,56].

High-throughput genomic technologies are advancing the understanding of microbial diversity in various environments [64]. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, enabling the construction of predictive models regarding metabolic potential and ecosystem-level interactions. These approaches facilitate the predictive phenotyping of organisms that are often difficult to study genetically or are uncultivable. Currently, there are approximately 600 finished or permanent draft acidophile genomes, including 184 extreme acidophile genomes (optimum pH ≤ 3.0) and 15 eurypsychrophilic acidophile genomes, which with a wide temperature tolerance are able to grow at temperatures above and below 15 °C but with a maximum growth temperature of 30 °C [42]. By elucidating correlations among transcriptomic data, biochemical parameters, and microbial succession during chalcopyrite bioleaching, experimental evidence has shown how microorganisms in co-culture communities adapt to the bioleaching environment early on and develop resistance to the toxic environment through their inherent functional properties [59]. Proteomic data offer insights into genome type and activity simultaneously, and strain-resolved community proteomics serves as a valuable complement to cultivation-independent genomic (metagenomic) analysis of microorganisms in natural environments [65]. Single-cell sequencing allows researchers to study the genetic material (DNA or RNA) of individual cells separately [61]. This technology provides insights into cellular heterogeneity, identifying rare cell types, understanding gene expression patterns at a single-cell level, and uncovering genomic variations within complex biological systems.

4.2. Structure and Reaction of Minerals

The leaching performance and extraction efficiency of minerals can be influenced by their structural characteristics, thereby impacting process control. Distinct types of minerals possess varying crystal structures and chemical compositions, which can impact reaction kinetics and the formation of products during the leaching process. Various tools have been employed to investigate the structure and leaching mechanisms of minerals (

Table 2. Tools for research on structure and reaction of minerals.

Tools	Function	References
Density functional calculation	Mechanism and energetics oxidation reactions by predicting reaction pathways, intermediate species, and reaction energies	[66]
Mössbauer spectroscopy	Provide information on the oxidation state, valence, and crystallographic environment of specific types of atoms in a material	[67]
X-ray diffraction (XRD)	Determine the crystal structure and composition of minerals by illuminating a sample and measuring its scattered light	[68]
X-ray photoelectron spectroscopy (XPS)	Detect chemical composition and electronic states of the surface of a material	[69]
X-ray absorption near-edge structure (XANES)	Provide information about the local electronic and geometric structure of atoms in a sample	[70]
X-ray fluorescence spectrometer (XRF)	Quickly measure the elemental content of minerals	[69]
Nuclear magnetic resonance (NMR)	Analyze the crystal structure and chemical composition of minerals and understand the position and orientation of ions within them	[71]
Time-of-flight secondary ion mass spectrometry (TOF-SIMS)	Provide information on the chemical composition and distribution of materials at the submicron scale	[72]

). These investigative methods provide valuable insights into the structure and behavior of minerals during leaching processes, facilitating a better understanding of leaching mechanisms and aiding in process optimization.

Mössbauer spectroscopy, for instance, analyzes the specific absorption of γ-rays by 57Fe to obtain information about the redox state of iron, mineral identity, crystallinity, and particle size. It has been used to determine the valence state of iron (Fe) in chalcopyrite as Fe (III), confirming the presence of trivalent iron and suggesting little to no spin canting, thereby indicating the presence of copper in the form of Cu (I) [67].

X-ray photoelectron spectroscopy (XPS) is commonly used to identify iron and sulfur species, such as the dissolution of chalcopyrite containing sulfur and ferric sulfate, which shows similarity to jarosite [73]. Jarosite accumulation can prevent further oxidation of chalcopyrite. X-ray diffraction (XRD) and X-ray fluorescence (XRF) spectrometry are also commonly used to identify oxidation products on the mineral surface. XRF spectrometry allows for quick elemental composition analysis of the reacted surface. XRD can determine mineral identity as well as provide information about average crystallite size and crystallinity [74]. X-ray absorption near edge structure (XANES) spectroscopy offers advantages over XRD as it provides insights into chemical speciation, studies amorphous materials, reveals local structure, and detects smaller amounts of a material [70].

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been used to qualitatively characterize various fracture planes of freshly cleaved chalcopyrite particles before and after hydrometallurgical treatment (leaching) [72]. This technique reveals that certain areas exhibit contamination from atmospheric hydrocarbons upon fracture, while others show high reactivity and minimal adventitious hydrocarbon contamination.

4.3. Microbial–Mineral Interaction

Research on microbial–mineral interaction was carried out to illustrate the contact mechanism of microbes on mineral dissolution (

Table 3. Tools for research on microbial–mineral interaction.

Tools	Function	References
Confocal laser scanning microscopy (CLSM)	Detect cellular structures, subcellular components, and the spatial distribution on minerals	[75]
Fluorescence in situ hybridization (FISH)	Specifically target and bind to the ribosomal RNA (rRNA) of the microorganisms of interest	[76,77]
Atomic force microscopy (AFM)	Observe and measure surface properties and morphology of samples at the atomic scale	[78]
Transmission electron microscopy (TEM)-EDS	Provide high-resolution images for studying the surface morphology, internal structure, and composition of minerals	[79]
Scanning electron microscopy (SEM)-EDS	Analyze the crystal lattice structure and micro-area chemical composition of minerals	[80]
Fourier transform infrared spectroscopy (FTIR)	Identify functional groups and chemical bonds in a material	[81]
Raman spectroscopy	Absorption of specific wavelengths by certain bonds enables the identification of minerals	[82]

). The application of confocal laser scanning microscopy (CLSM) and fluorescence in situ hybridization (FISH) by specific DNA-binding fluorescent probes enables the localization and quantification of specific microorganisms in laboratory and environmental samples [75,76]. CARD-FISH is an improvement over traditional FISH especially suitable for aquatic habitats with small, slow growing, or starving bacteria, in which the signal intensities of hybridized cells is frequently below detection limits or lost in the high fluorescence background of dense mineral matrixes [77].

Atomic force microscopy (AFM) is usually applied to observe and measure the surface properties and morphology of samples at the atomic scale, and it can show very clearly the size and shape of the microbes and mineral surface [83]. Transmission electron microscopy with energy dispersive X-ray spectroscopy (TEM-EDS) and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS) analysis can provide high-resolution images for studying the surface morphology, internal structure, and composition of minerals [84]. TEM is ideal for investigating atomic-scale structures, crystal defects, and interfaces, while SEM excels in surface morphology characterization, elemental analysis, and three-dimensional imaging of larger samples. Researchers often use these techniques together to gain a comprehensive understanding of sample properties and structures from the atomic scale to macroscopic features.

Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy were applied to identify the functional groups [85]. FTIR measures the absorption or transmission of infrared radiation by a sample, which is related to the vibrational modes of the molecules in the sample. Different chemical bonds in a molecule absorb infrared radiation at specific frequencies, so FTIR can be used to identify functional groups and chemical bonds in a material. FTIR can also provide information on the molecular structure, conformational changes, and intermolecular interactions of molecules in a sample. For example, it identified the oxidation behavior of sulfur-oxidizing bacteria (A. thiobacillus) and detected two types of spectral shifts resulting from sulfide mineral adsorption, providing a basis for the hydrogen bonding mechanism [81]. Raman spectroscopy provides information on molecular vibrations in the sample that are not detected by FTIR, such as those involving polarizable groups. Normal Raman spectroscopy, combined with electrochemical techniques, has been shown to be a powerful tool for investigating the macro oxidation products of mineral sulfides [82]. The photo-induced product yielded a Raman spectrum consistent with polymeric sulfur and it is concluded that the parent compound is a metal-deficient sulfide having a remnant chalcopyrite lattice structure [82].

4.4. Particles and Aggregation States

There is always a decision to be made regarding the crush size for heap leaching. This decision involves balancing the slow rate and limited extent of leaching from large particles against the cost of crushing finer particles, as well as considering the permeability of the heap based on different ore sizes. During the early stages of heap leaching technology development, ores were crushed to small sizes. However, this resulted in poor permeability. To address this issue, the concept of thin layer leaching was developed in the 1980s primarily for copper oxides, and was later historically applied to copper sulfides. This development played a crucial role in the remarkable expansion of heap leaching, solvent extraction, and electrowinning processes in South America. In recent years, heap leaching has been characterized by the use of relatively coarse particle sizes [9,47]. Typically, crushed and agglomerated ores have a top size of 12–25 mm, while run-of-mine dump leaching operations use even larger particles. Smaller particles may have higher leaching efficiency, but they can also become compacted and impede the flow of the irrigated solution.

The overall rate at which a mineral is dissolved from an ore particle is quite often the manifestation of a complex network of individual phenomena, each proceeding at its own intrinsic rate. For finely ground particles, such as those in tank leaching, leaching rates are typically controlled by the intrinsic kinetics of mineral dissolution. In heap leaching, however, mineral grains are usually embedded within larger ore particles or agglomerates, and thus leaching happened firstly by solution diffusion through a network of pellet pores, then by mineral dissolution, and then the diffusion of the pregnant solution outwards [12].

The particle size and aggregation states determine the inner diffusion and outer diffusion of the gas and solution in heaps (Figure 3). Agglomerates resulted in small ore particles clumping together due to the solution’s interaction with the particle surfaces, which made the channels within the heap carve out pathways between the particles [46]. This includes the study of ore and particle properties, visualization techniques for ore characterization, and the connection between comminution and leaching behavior, as well as particle models within heap leach modelling. Particles with irregular shapes and size distribution can create voids or blockages that impact the leaching efficiency.

4.5. Multiphase Flow Transfer

Heap leaching involves multiphase flow transfer, which means that the solvent solution, gas, and solid particles are interacting with each other in a complex manner [86]. The velocity within the heap is influenced by the size and shape of the particles, and the packing density of the bed. The solution passes through according to the velocity, and interacts with the ore to dissolve the valuable metals, and plays a significant role in determining the extraction efficiency and the overall performance of the heap leaching process [87]. The gas helps to oxygenate the solution, which improves the chemical reactions between the ore and the solvent solution, leading to higher metal extraction yields. The velocity and distribution of the gas flow affect the aeration rate, the residence time of the solution in the heap, and the temperature and humidity of the system. This occurs as the gas flows through the pore spaces between the particles, affecting the distribution of the solution. The gas and solution flow can also cause particle motion, leading to compaction or segregation of the solids [88].

Overall, the multiphase flow transfer in heap leaching is highly complex and can be challenging to predict and control. Proper design and optimization of the heap geometry, aeration rate, and hydraulic properties are essential for maximizing metal recovery while minimizing operational costs. Advanced computational models and experimental techniques are often used to improve understanding and optimize the heap leaching process [89,90].

The heat generated by the chemical reactions between the sulfide ore and the solvent solution can cause the temperature within the heap to rise, which can impact the leaching kinetics and the solubility of the metals [91]. In addition to heat generation from chemical reactions, heat transfer can also occur due to changes in ambient temperature. This can happen when the heap is exposed to direct sunlight or during periods of extreme weather conditions, as well as water evaporation.

4.6. Leaching Tests and Modeling

Laboratory leaching tests are vital in developing an efficient heap leaching process (

Table 4. Tools for laboratory experiment and modelling of heap bioleaching.

Tools	Function	References
Roller bottle tests	Quick tests for the recoverable metal at a given ore size and condition	[92]
Column tests	Simulate heap leaching to figure out the leaching rate and final recovery	[93]
Permeability tests	Test the permeability of the ore at given size distribution and condition	[94]
Mini heap tests	Closer to industrial heaps to verify some operation parameters	[36]
Modeling	Predicts the behavior of bioleaching processes under different conditions, for scaling up, efficiency elevation and cost reduction	[95]

). These tests play a crucial role in identifying potential challenges and optimizing critical operational parameters to ensure successful metal recovery. Given the enormous size of heaps, regulating them during leaching is challenging, making thorough and systematic laboratory testing necessary and important before industrialization.

One commonly used method for quick metal-recovery tests is roller-bottle tests [92]. These tests determine the amount of metal that can be extracted from the ore under different conditions such as solution concentration, temperature, and pH. Roller-bottle tests can provide information about leaching kinetics and metal solubility at low operational costs, but cannot simulate the conditions under the stacking pile.

Column leach tests involve irrigating a column filled with crushed ore to simulate the heap leaching process [93]. These tests assess the hydraulic and metallurgical characteristics of the ore and optimize the design and operation of heap leaching. Column leach tests provide detailed information about flow rates, solution distribution, and retention time, helping predict the rate and extent of metal recovery during heap leaching and ensuring efficient operation.

Permeability tests measure the ore’s ability to allow fluid flow through under stacking pile conditions [94]. Understanding the hydraulic properties of the ore helps optimize the irrigation rate and strategy, ensuring proper solution distribution throughout the heap while minimizing operational costs. Adjustments to irrigation rates may be necessary based on the permeability of the ore, avoiding both insufficient and excessive solution application.

Before industrialization, mini heap leaching tests are usually conducted [94]. Factors such as temperature, pH, moisture content, oxygen supply, and nutrient availability are usually controlled during the construction and operation of a bioleaching mini heap. Monitoring and sampling techniques are employed to assess metal recovery rates and microbial activity within the mini heap. The use of a bioleaching mini heap allows researchers and operators to evaluate the feasibility and efficiency of bioleaching processes on a smaller scale. It enables optimization of operating conditions, exploration of different microbial consortia, investigation of leaching kinetics, and assessment of potential environmental impacts before scaling up to larger industrial operations [36,96].

Heap leaching operations are complex but versatile unit operations that require sophisticated modeling tools for effective design and operation [97]. Mathematical models consider the solid phase (ore particle size distribution), liquid phase (leaching solution), and gas phase (air and air pockets) at the agglomerate scale. The diffusion–reaction equation models leaching at the ore particle level, while oxidation by attached and detached microbes is treated separately. A procedure has been proposed to extrapolate laboratory column leaching kinetics for commercial heap leaching design, aiding in process optimization [98].

4.7. Industrialization and Operation Optimization

The laboratory tests provide crucial design parameters, considering the physical, chemical, and microbial aspects of heap bioleaching. However, when transitioning to industrial-scale operations, the challenges specific to heap bioleaching industrialization must be addressed [98].

Important process parameters must be fully considered, including the choice between single-layer or multi-layer heap modes, agglomeration techniques, crushing size, and irrigation rates, all of which have implications for industrial operations [35]. Acid consumption, neutralization, and expected recovery should also be carefully evaluated for the economic viability of heap leaching.

During heap bioleaching, solution assays are performed to calculate copper recovery, serving as the basis for decisions on new cells or layer additions. In some cases, detectors can be buried in heaps to assay the solution and measure gas parameters for reference. After heap leaching operations, examination of the heaps and testing of leach residue are conducted to determine copper recovery and evaluate economic aspects.

In full-sized heaps, the actual recovery is often lower than predicted from column tests [90]. Optimizing of heap leaching processes is conducted to improve industrial recovery and align it more closely with test results. It involves addressing multiple factors and striking a delicate balance to achieve higher efficiency and economic viability. Various optimizations are carried out to enhance leaching efficiency, focusing on heap physical characteristics, solution chemistry, and microbial activity (

Table 5. Industrial factors and parameters influencing heap bioleaching efficiency, summarized from [1,12,37,99].

Heap Physical Parameters	Solution Chemical Parameters	Microbial Regulation	Other Operations
Mineral type	pH	Microbial community composition	Leaching mode (single layer or multi layers)
Grain size	Redox potential	Microbial abundance and activity	Irrigation rate and intervals
Mineral dissemination	Oxygen content and availability		Rehandling
Ore size distribution	Carbon dioxide content		Solvent extraction operation
Permeability	Fe concentration		Solution neutralization and purifying
Porosity	Other impurities		Aeration
Temperature

) [1,12]. For instance, achieving higher recovery rates may require a smaller grain size, but excessively fine particles can result in low permeability, leading to industrial failure. Striking a balance between permeability and mineral exposure is a top priority, though this is challenging to test in laboratory settings like column leaching and permeability tests. To promote microbial activity, solution impurities and acidities sometimes are neutralized and discharged to maintain favorable conditions. Additionally, higher heap porosity is important for microbial growth. At times, ore is rehandled by excavators after a leaching period to increase permeability and copper recovery. Maintaining acid and iron balance in the heaps is also crucial. Some heap solutions may have excessive acidity and iron due to pyrite oxidation [47], while others require sulfuric acid addition to maintain desired acidity levels. Pyrite oxidation regulation can help manage acid and iron balance, significantly reducing acid addition and neutralization costs [9].

5. Challenges in Heap Bioleaching Technology Development

Despite the industrialization of heap bioleaching worldwide, there are still numerous challenges associated with its development and implementation. It still faces limitations such as low recoveries, long extraction times, and high operational costs. Therefore, there is a need to optimize heap operations and reduce extraction operating costs.

Heap bioleaching involves biological and chemical reactions, and multi-phase mass transfer of gas, solution, and solids, as well as heat transfer [12]. This optimization process requires an understanding of the interactions between physical, chemical, and biological processes within the heap [9,43,47] (Figure 4).

Maintaining optimal conditions for microbial activity, solution chemistry, heap physicality, and mineral exposure simultaneously is challenging. Proper ore crushing is critical for mineral exposure to the extractant, balancing between sufficient exposure and heap permeability. Biological activity accelerates sulfide mineral dissolution, influenced by heap conditions and solution chemistry, while some ores contain inhibitors or toxic byproducts affecting leaching [43,100]. Also, the physical condition, which is influenced by ore characteristics and industrial operation, can significantly influence solution chemistry and microbiology [101].

Scaling up of heap bioleaching from lab to industrial scale requires addressing varied microbial performance, leaching kinetics, and heap properties [98]. Temperature control in open-air settings is crucial but challenging due to environmental factors. Advanced modeling and experimental methods are key to optimizing heap bioleaching for maximum metal extraction.

6. Future Trends in Research and Industrialization of Heap Bioleaching

With the increasing focus on achieving net-zero carbon emissions, there is a growing emphasis on transitioning to a low-carbon economy. Heap bioleaching, particularly in the field of biohydrometallurgy, holds great potential due to its environmentally friendly separation conditions. This includes low energy consumption during ore commination, lower leaching temperatures, and reduced leaching facilities. Although heap bioleaching is currently predominantly used in the industrialization of primary copper (secondary ore), gold, and uranium ores, there is a need for further development and adaptation to encompass a broader range of resources. This includes primary copper ore, zinc, cobalt, and nickel ores, as well as waste resources [3].

The efficiency of bioleaching microbes remains a significant challenge in the bioleaching process, as their performance in iron and sulfur oxidation is not yet optimal. Additionally, inhibitory elements in complex ores or accumulated during solution cycling can hinder their effectiveness. To overcome these challenges, it is essential to develop more efficient bioleaching microbes from stressed environments, such as highly acidic and low-temperature conditions [102]. Synthetic biology and genetic engineering offer promising avenues for achieving this goal [103,104]. Synthetic approaches can be utilized to enhance the capabilities of microbes, enabling them to more efficiently oxidize iron and sulfur while also improving their resistance to stress. These advancements will be crucial for the further implementation of heap bioleaching.

Heap bioleaching is a multidisciplinary field that requires expertise in various disciplines such as mineralogy, heap physical characteristics, solution chemistry, and microbiology. Collaboration among scientists from diverse fields including geology, mineralogy, biology, microbiology, chemistry, and hydrology is essential to drive technological advancements. It is also recommended to establish synergistic collaborations between scientists, industries, and software providers specializing in modeling, plant automation, and control systems. This collaborative approach can improve process efficiency, effectively manage big data using advanced tools like data analysis, machine learning, and digital twins, and enhance operational performance and the scale-up of bio-oxidation technology. Resolving mesoscale issues between different scales is also crucial. Prior to industrial application, efforts should be dedicated to bridging the gap between fundamental and applied research, tackling technological and economic challenges, and prioritizing environmental and ecological risks while adhering to strict safety and ethical regulations.

Bio-oxidation has numerous applications, and it generates a substantial amount of data that can be utilized for process improvement. By combining advanced models, equipment, and effective management of big data from laboratory to pilot scale, monitoring can be enhanced, and optimal results can be achieved through experimental validation. Successful projects like the Escondida Mine [105] have demonstrated the establishment of Decision Support Systems based on historical operations. Machine learning and artificial intelligence techniques can be employed to optimize bio-oxidation in both heap and reactor processes. Additionally, intelligent systems leveraging AI and big data analysis can forecast and simulate data, thereby enhancing the accuracy and reliability of the heap leaching process.

Automation and intelligentization are key trends in the mining industry for improving the heap leaching process. These technologies offer benefits such as enhanced production efficiency, cost reduction, carbon emissions reduction, and improved safety. Automation can be achieved through the use of robots and other equipment capable of performing tasks like terrain measurement, plant growth monitoring, and automated ore conveyance. Automated control systems can adjust parameters such as temperature, humidity, and pH value to optimize metal extraction. Intelligentization technology involves the monitoring and analysis of flow data through the use of sensors that collect information on temperature, humidity, oxygen content, pH values, and more. This data is then automatically processed by a computer to optimize heap leaching parameters, resulting in improved production efficiency and reduced losses.

Heap bioleaching is surely advancing with optimized microbial consortia and modern genetic tools to enhance metal leaching, and extending by collaboration with researchers of multi disciplines to optimize the process and apply it to a wider range, and further optimization with big data, automation and intelligentization.