Keywords

17.1 Introduction

Metals are essential for economic growth and modern society. Global resource use is expected to double in the period 2010–2030, while the quality and grade of ores have declined over time (Kinnunen and Kaksonen 2019). Biomining has enabled the extraction of value from low-grade resources, the utilisation of which would not necessarily be feasible through traditional pyrometallurgical or hydrometallurgical processing. However, many techno-economic challenges associated with established biomining processes remain and need to be understood and addressed, not only to consolidate biomining as a technology of choice in the conventional mining context, but also to facilitate its successful extension into novel applications and resources.

As conventional mineral resources are becoming increasingly depleted and/or more complex, there has been growing interest in the exploration of deposits in the continental deep subsurface, deep sea, and outer space. Moreover, metal-containing wastes are increasingly considered valuable secondary resources that have not yet been extensively exploited, and the utilisation of which would improve the sustainability of mining industry (Kaksonen et al. 2020).

The application of biomining to new types of mineral resources may also expand the range of biotechnologies being considered for metal extraction and recovery. Novel biolixiviants can provide more environmentally friendly alternatives to chemical leaching agents, whereas “phytomining” may facilitate both metal extraction and remediation of mine sites. Techniques such as bioflotation, biosorption, and biomineralisation are gaining renewed interest as potentially sustainable techniques to complement bioleaching. This chapter aims to offer an outlook towards future biomining, starting with a brief review of the mechanisms and limitations of bioleaching processes and from there expanding into an overview of new avenues.

17.2 From Understanding the Rate Limitations of Bioleaching Mechanisms to Improved Process Design

The various sub-processes that govern metal sulfide bioleaching and their complex interactions in various bioleaching processes have been discussed in Chaps. 2–5 and are also summarised in Petersen and van Staden (2019) and Petersen (2010a). Figure 17.1 offers an illustration of this network of interactions. The overall dynamics of a leaching system are determined by the relative dynamics of the individual steps and sub-processes in such a way that the overall rate (or “speed”) of a given bioleaching process is governed by the slowest step in the network of interactions.

Fig. 17.1
A schematic is split into solid, aqueous, and gaseous. Aqueous region is separated from the solid region by a biofilm or E P S layer. Mineral and gangue acid dissolution happens in the metal sulfides. These ions are transported to the aqueous and gaseous regions through the pores. Oxygen and carbon dioxide flow from gaseous to aqueous region.

Schematic view of physical/chemical and biological interactions in metal sulfide bioleaching. EPS = extracellular polymeric substances

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The design of bioleaching processes is concerned with sizing of equipment and drawing up of operating schedules to achieve maximum extraction of elements of economic interest at the fastest rate. In the applied context, however, considerations of costs to build and operate a given process and the size of the operation, critically determine what is economically feasible compared to what is technologically possible.

Bioleaching processes tend to be significantly slower than their conventional chemical counterparts, and it is this aspect, and the subsequent requirement for larger tankage to achieve the same throughput as a competing process, which have commonly limited the broader uptake of bioleaching technology in industrial practice. It is, therefore, critical to understand the factors affecting bioleaching rates and yields in order to maximise cost-effectiveness in a given processing context for the future establishment of bioleaching technologies.

A key rate-limiting step in bioleaching is the transfer of oxygen and CO2 from the gas phase into aqueous solutions. In tank bioreactors this is achieved through the injection of air bubbles and vigorous agitation, creating a large gas–liquid interface. However, this comes at the cost of energy input into agitators and compressors. Also, due to hydrodynamic stress experienced by microorganisms at vigorous agitation, there is a need to maintain relatively dilute slurries in tank reactors, meaning the volumes of water handled per unit weight of mineral feed are relatively large, affecting the size of both primary and downstream equipment for metal recovery.

The effective solid-to-liquid ratio is much more favourable in heaps, but here the channelling of gas through the wet ore bed is relatively difficult to achieve and control. This is primarily due to the significant non-homogeneity of the ore packing and solution distribution. Even under the most optimal conditions, the gas–liquid interface is relatively small, resulting in significant rate limitations of the process (Petersen 2010b).

Inner-particle diffusion through narrow pore spaces is a slow process, and the time to diffuse increases with the square of the particle radius. In heap leaching this sets up a complex trade-off in terms of the particle size distribution of the ore being leached—crushing finer will reduce diffusion time but risks creating a more compact bed through which gas and solution channel less easily, while also incurring a higher cost for ore preparation. Fine crushing can also impact heap stability, leading to engineering failures such as subsidence of sidewalls.

Further factors to consider are microbe–mineral interactions and the relative kinetics of microbial processes to provide reagents (i.e., sulfuric acid and ferric iron for sulfide minerals) and that of mineral dissolution, which consumes these reagents. At steady state these two processes operate at equivalent rates. The position of this balance strongly depends on local solution chemistry which influences both processes (effect of dissolved oxygen, CO2/carbon source, substrate, toxic ions, etc., on the biological reactions, oxidant, complexing agent, etc., on the mineral reaction, as well as pH, solution oxidation–reduction potential (ORP) and temperature on both reactions). As with the supply of oxygen, control of the chemical conditions is more easily achieved to be at their optimum in tank reactor operation, whereas in heaps any sort of local control is essentially impossible, making it all the more critical that external operating parameters (such as irrigation and aeration rates and modes; Chap. 2) are chosen and manipulated such that optimal operating conditions are maintained in the heap throughout and over the entire period of its operation. This necessitates the use of a comprehensive mathematical model of the process (Petersen and van Staden 2019; Chap. 2).

The time to complete extraction has a critical influence on process costing for the treatment of primary ores since the cost for producing the feed material must be borne upfront, whereas revenue is generated only after extraction and recovery. Thus, material held up in the process represents an inventory cost, which can make heap leaching uncompetitive, if alternative processing options are feasible, despite the much lower capital and operating costs of its operation. Similarly, the need for large tanks to accommodate long residence times in relatively dilute slurries limits the viability of the process.

Future technological development of biomining, therefore, needs to address the key issues that limit the rate of the process, such as supply of oxygen and CO2, process intensification in tanks, and packing/permeability/particle size in heaps. In the light of this, agitator design for tank leaching continues to improve, whereas the design and operation of heaps (particularly copper sulfides) have moved to using smaller top particle size in more carefully stacked heaps, controlled intermittent irrigation to achieve uniform wetting and permeability in heaps, as well as rigorously designed aeration systems. Temperature control to achieve within the heap conditions suitable for thermophilic acidophiles for effective bioleaching of chalcopyrite has been shown to be possible but requires a systematic understanding of the thermal interactions within the heap based on comprehensive mathematical models.

The “speeding up” of a biomining process often involves financial trade-offs, as improved extraction does not necessarily justify the means required to achieve it. In an industrial bioleaching context, the cost of processing is ultimately limited by the value of the metal extracted. This trade-off can be successful for biomining, especially in the context of gold: its high value in relatively small volume operations creates a favourable niche for biological extraction. Similarly, carefully designed and operated heap bioleaching offers favourable opportunities for the extraction of low-grade minerals, especially chalcopyrite, complex minerals such as shales, or enargite and other minerals containing toxic elements that make them unsuitable for conventional processing. It is probable that future developments of biomining technology will focus on these areas.

Process economics are somewhat different in bioremediation applications, where there is less of a short-term incentive but more of a long-term benefit through the destruction of negative value associated with disposal of the untreated material. In this context, the slowness of heap leaching would not present an inventory cost and therefore make it an interesting option to consider more systematically.

A hybrid scenario exists in the context of biomining waste materials from mining and mineral processing, where the focus is on recovering remaining metal value and simultaneously remediating the residual waste. There is little cost associated with preparing the feed material, as its mining from surface deposits is usually straightforward, and it is already available in a granular form. Copper heap and dump bioleaching in their current form fall into this category, but similar opportunities exist for many concentrator tailings materials from base metal sulfide ores, providing the challenge of agglomerating the finely ground tailings onto stable “particles” suitable for heap leaching can be addressed.

Many other options for biomining for metal production in the future are discussed in the following sections, but these still need to be assessed in light of the processing challenges outlined above. The success of harnessing new mineral resources for biomining, employing new bioleaching chemistries, and implementing new biotechnologies critically hinges on their industrial application offering a competitive opportunity to provide resources in a sustainable manner.

17.3 Biomining Unexploited Mineral Resources

Industrial-scale bioleaching processes have so far mainly targeted relatively shallow sulfide mineral deposits that can be easily accessed by open cut or underground mining. The depletion of these mineral ores has triggered the search for alternative resources that could be amenable for metal extraction. Among these are ore deposits in deep continental subsurface and deep sea environments, extraterrestrial bodies as well as metal-containing mining, metallurgical and postconsumer wastes (Kaksonen et al. 2020).

17.3.1 In Situ Biomining

Conventional mining processes rely on drilling, blasting, excavating, and hauling ores to the surface before reducing particle size through crushing, and in some cases grinding, before metal extraction. This ore preprocessing has been estimated to represent 5–7% of global energy consumption, and the recovered metals often account for less than 1% of the excavated material (Johnson 2015). Deposits at depths of one or more kilometres are typically not considered to be accessible or economical for extraction using conventional mining methods, with the exception, perhaps, of precious metals. In situ recovery aims to extract metals from deep underground deposits without bringing ore to the land surface, thus reducing energy consumption, costs, above-ground footprint, and mine waste generation. Some form of in situ recoveries of copper has been practiced since medieval times, but the role of microorganisms in metal solubilisation was not known until the 1950s. The intentional use of microbial catalysts for in situ recovery has been explored since the 1970s, first for uranium and later for base metal extraction (Chap. 1).

The term deep in situ biomining (DISB) has been used to describe an emerging in situ biomining approach that targets fractured ore bodies at depths of 1–2 km. The approach utilises spatial separation of unit processes for (1) chemical underground leaching of metals from sulfide ore under saturated conditions with acidic ferric lixiviant delivered through boreholes, (2) above-ground metal recovery from pregnant leach liquor, and (3) biological lixiviant regeneration in an above-ground bioreactor (Fig. 17.2a; Johnson 2018). DISB has been recently explored in the European Union-funded BIOMOre project, which targeted a copper-containing saline and calcareous “kupferschiefer” deposit in Poland. The extraction of copper from the deposit required a three-step approach in which first water and then acid leaching was used to remove excess salinity (which would otherwise inhibit microbial activity) and acid-consuming materials, respectively, before bioleaching with biogenic ferric lixiviant (Fig. 17.2c; Johnson 2018). The use of biogenic ferric lixiviant could also be used for oxidising refractory gold ores in an in situ environment before leaching the gold with thiosulfate or iodine-based lixiviants (Fig. 17.2d; Kaksonen et al. 2014b; Kaksonen et al. 2020).

Fig. 17.2
Diagram A and B are steps in saturated and unsaturated in situ blooming. They have Leach block, solution injection, and recovery. Air enters the bioreactor in A and leach slope in B. Diagram C depicts the three stages of copper leaching. Diagram D represents the three stages of gold leaching from pyrite oxidation after acid leaching.

Various in situ biomining approaches: (a) Deep in situ biomining under saturated conditions utilising biogenic ferric iron regenerated above ground; (b) in situ biomining under unsaturated conditions utilising in situ aeration and biogenic ferric regeneration in an underground stope; (c) in situ biomining of copper from a saline calcareous copper sulfide ore; (d) in situ leaching of gold from refractory sulfidic deposit after biological pre-treatment [adapted from Kaksonen et al. (2020) and Vargas et al. (2020)]

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An alternative in situ biomining approach is based on forming a subsurface ore bed with sufficient permeability to operate it as an unsaturated trickle-bed bioreactor that allows in situ regeneration of the biogenic ferric iron lixiviant with underground aeration (Fig. 17.2b). Free-face blasting and underground galleries (stope leaching) have been proposed to enable the partial removal of the ore for this type of configuration. Based on modelling, this approach would allow the leaching of taller ore beds than the saturated leaching that relies on above-ground ferric lixiviant regeneration. Moreover, this approach avoids the need for an above-ground bioreactor, although the ore body pre-treatment costs are higher than in saturated leaching because of the need to remove a fraction of the ore (Vargas et al. 2020). An in situ aeration concept has also been explored for the biological oxidation of refractory sulfidic gold ores before possible chemical in situ leaching of gold (Kaksonen et al. 2014b). The simulated in situ aeration enhanced pyrite oxidation during leaching of the pyrite with biogenic ferric lixiviant. One advantage of using microbial catalysts for in situ leaching as compared to chemical ferric leaching is the ability to remove passivating sulfur layers from the mineral surfaces through microbial oxidation as some bioleaching microorganisms can oxidise reduced sulfur compounds with ferric iron as the electron acceptor (Kaksonen et al. 2014b).

17.3.2 Deep Sea Biomining

Deep sea minerals were first discovered in 1873, but their economic potential for mining was only proposed in 1965. Since then, deep sea minerals have attracted attention as alternative sources of metals to terrestrial ore deposits (Sharma 2017). Examples of minerals of interest include polymetallic nodules, ferromanganese crust, and hydrothermal vent sulfides. Hydrothermal vent sulfides are rich in barium, copper, gold, lead, silver, and zinc and once brought to surface could potentially be processed using oxidative bioleaching processes for base metal extraction and precious metal liberation. Polymetallic nodules contain copper, cobalt, nickel, and zinc, typically in the lattice of manganese and iron oxide/hydroxide phases. Other elements of interest in nodules include molybdenum, rare earth elements, platinum, and tellurium (Kaksonen et al. 2020). The bioleaching of these minerals requires reductive bioleaching (Chap. 15). Manganese nodules have also been explored as an oxidant for chalcopyrite bioleaching (Kaksonen et al. 2020). Ferromanganese crust contains negatively charged Mn-oxyhydroxides that are bound to hydrated cations (Ca, Ni, Zn, Pb) or to positively charged Fe-hydroxides, which are complexed with anionic forms of As, P, V, and other elements (Wang and Müller 2009).

The utilisation of deep sea minerals is subject to technical, economic, legislative, environmental, and other challenges. The minerals are typically located at relatively deep locations, e.g., crust at depths of 800–2400 m, hydrothermal vent sulfides at 1000–2000 m (Wang and Müller 2009), and polymetallic nodules at 4000–6500 m (SPC 2013; Fig. 17.3). Hence, the mining of deep sea minerals requires underwater robots and pumping the minerals as slurry to the surface for metals extraction and recovery (Kaksonen et al. 2020). The profitability of deep sea mining operations is influenced by the discovery of other mineral deposits which impacts metal prices (SPC 2013). An advantage of biomining processes is that they can be easily used at a small scale and hence may be economically more feasible for small deposits than conventional metallurgical processes. As many of the deposits are located in international waters, their utilisation is regulated under the United Nations Convention on the Law of the Sea through the International Seabed Authority (Sharma 2017). The utilisation of deep sea minerals has also raised concerns about the potential impact of the activities on marine ecosystems (Kaksonen et al. 2020).

Fig. 17.3
A schematic. Minerals are present in the crust at 800 to 2400 meter, vents at 1000 to 2000 meter, and nodules at 4000 to 6500 meter. A sea-bed mining robot, attached to the production support vessel via riser pipe, is used to pump these minerals. A return water pipe is attached to the production vessel.

Mining of minerals from deep sea vents, nodules, and crust [adapted from Wang and Müller (2009) and SPC (2013)]

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17.3.3 Space Biomining

In situ resource utilisation (ISRU), the use of local resources for production and maintenance, is being explored to support space missions and human establishment in space. Large-scale inhabitation of space and space-based industries would need to rely on ISRU as resupply of resources from Earth is not practical nor economically feasible (Klas et al. 2015). Metals extracted from space minerals could be used for 3D printing structures, electronics, and spacecraft components to decrease the dependence of space activities on resources shipped from Earth and support human establishment beyond the lower Earth orbit. Lunar and Martian regoliths have been reported to contain SiO2, FeO, Al2O3, and MgO, and additionally TiO2 and Ca have been detected in Lunar regolith. Hydrated minerals have also been identified on both the Moon and Mars, suggesting a possible indirect source of water for in situ biomining operations (Bishop 2005; Hand 2009). Asteroids have been shown to contain platinum group metals (iridium, palladium, platinum, and rhodium) and 44 other “endangered” and “critical” elements that will face supply limitations in future years (Kaksonen et al. 2020).

The feasibility of using biomining as an enabling technology for ISRU is attracting interest. Biomining approaches proposed for space applications include, for example, oxidative and reductive bioleaching of metals for downstream recovery, bioaccumulation of iron in cells, for example as modified ferritin or magnetosomes to allow magnetic iron recovery, and partial biological iron oxidation or reduction to generate magnetite for magnetic recovery (Kaksonen et al. 2020; Volger et al. 2020a). Microorganisms investigated for space biomining include the ferrous iron- and sulfur-oxidising and ferric iron-reducing acidophile Acidithiobacillus ferrooxidans, ferric iron-reducing Shewanella oneidensis (Kaksonen et al. 2020), magnetotactic, magnetosome forming heterotrophic Magnetospirillum gryphiswaldense and genetically modified heterotrophic Escherichia coli which overexpresses a modified ferritin complex, and has an improved iron import mechanism and dysfunctional iron export mechanism (Fig. 17.4; Volger et al. 2020a).

Fig. 17.4
Diagram A to G are biomining types. The general formula starts with iron ions, reacting on microorganisms and oxygen to produce modified minerals. Diagram H depicts the production of edible plants from algae and biomining with heterotrophic microbes, light, nutrients, and carbon dioxide. Lactate, Regolite, and Biomass feed into mining.

Various approaches proposed for biomining of minerals in space (a–g) and an example of integrating biomining processes into other life-sustaining processes in space (h) [adapted from Kaksonen et al. (2020) and Volger et al. (2020a, b)]

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Space environments differ from Earth conditions in terms of gravity, pressure, radiation, temperature ranges, chemical composition, as well as water and nutrient availability (Klas et al. 2015). Space biomining studies have evaluated, e.g., the ability of biomining microorganisms to survive and grow on, and extract metals from, Lunar and Martian regoliths (Kaksonen et al. 2020; Volger et al. 2020a), the effect of microgravity on biomining microorganisms (Kaksonen et al. 2020), the effect of magnesium perchlorate, which is abundant in Mars, on biomining microorganisms (Volger et al. 2020a), bioreactor and process flowsheet development (Volger et al. 2020b) and payback times of biomining infrastructure (Volger et al. 2020a). Engineering challenges related to space biomining include, for example, the delivery and establishment of microbial communities in space environments, operational maintenance of microbial activities, processing, and refining of extracted resources and delivery of the products to end users (Klas et al. 2015). Robots will be essential for the implementation of ISRU in hostile space environments (Klas et al. 2015; Kaksonen et al. 2020). The use of natural resources in space is governed by the Treaty on Principles Governing the Activities of States in the Exploitation and Use of Outer Space, including the Moon and Other Celestial Bodies (Outer Space Treaty; Klas et al. 2015).

17.3.4 Biomining Waste Materials

Mining and mineral processing generate in the order of 100 billion tons of solids wastes annually. Examples of mining and metallurgical wastes include tailings, slags, converter sludges, and pyritic ashes. Biomining has been shown to be feasible for extracting metal values from minerals that could be considered as wastes due to grades that are sub-economic for traditional metallurgical processes. This enables the extension of mine life and the utilisation of deposits that would not otherwise be exploited. Bioprocessing can also make waste more amenable for final disposal, reducing risks to humans and the environment (Kaksonen et al. 2020).

Post-consumer wastes are another waste stream that can supplement declining primary ore grades and reserves and thereby support the circular economy (Chap. 14). Wastes that contain valuable metals include batteries, spent catalysts, electronic equipment (e-waste), magnets, light products, sewage sludge, municipal solid waste fly ash, and powerplant fly ash (Srichandan et al. 2019; Kaksonen et al. 2020; Yu et al. 2020). Depending on the products, these may contain precious, base, and critical metals. The complexity of the wastes, presence of hazardous substances, and relatively small waste volumes pose challenges for the use of traditional metallurgical approaches for value recovery, and biohydrometallurgy is increasingly being considered as a sustainable alternative for extracting metal values locally from these waste streams. The economic feasibility of biotechnical, and non-biological, metal extraction and recovery methods depends on waste volumes, their content of metals and impurities, geographic location, transport distances, capital and operating costs, environmental impacts, and regulatory framework including landfill and export bans, and incentives for resource recovery (Reuter et al. 2018; Kaksonen et al. 2020). Therefore, the competitiveness and sustainability of biomining approaches for waste processing need to be evaluated on a case-by-case basis.

A number of laboratory- and pilot-scale studies have been conducted to explore biological extraction and recovery of metal values from wastes [reviewed in Srichandan et al. (2019), Yu et al. (2020) and elsewhere]. Approaches evaluated include, e.g., biodismantling printed circuit boards (Monneron-Enaud et al. 2020), bioleaching with various biolixiviants, bioelectrochemical systems, biosorption, and biomineralisation (Yu et al. 2020). One-step, two-step, and spent medium bioleaching have been explored to alleviate toxicity of some wastes to microorganisms and to identify possible leaching mechanisms. Moreover, due to the complexity of wastes, the integration of various biological, chemical, and/or physical unit processes may be required for value recovery (Kaksonen et al. 2020). An example of the integration of chemical and biological unit processes is the pilot-plant of Mint Innovation, a start-up company in New Zealand, that leaches metals from e-waste using chemical leaching and recovers gold from leach liquors through biosorption with Cupriavidus metallidurans (Kaksonen et al. 2020).

17.4 Unconventional and Emerging Biotechnologies for Extracting and Recovering Metals

17.4.1 Bioleaching with Unconventional Lixiviants

Biogenic Organic Acids

While much of biohydrometallurgy has focused on the biologically facilitated oxidation of sulfide minerals, many metals are derived from oxide-type minerals through acid leaching. This acid could be generated from the bioleaching of acid-generating minerals, such as pyrite, elemental sulfur oxidation, or through the production of biogenic organic acids, such as acetic, citric, oxalic, or polyphenolic acids (Ilyas et al. 2018). While organic acids do not deliver the same acid strength as inorganic acids, they can form organic complexes with metal ions, often rendering them soluble in solution where an inorganic acid would not. A key example is lead, which is insoluble in sulfate systems, but well soluble in the form of lead acetate [and similar for lead citrate and oxalate]; reaction (17.1):

$$ \mathrm{Pb}\mathrm{O}\left(\mathrm{s}\right)+2\ {\mathrm{CH}}_3\mathrm{COO}\mathrm{H}\ \left(\mathrm{aq}\right)\to \mathrm{Pb}{\left({\mathrm{CH}}_3\mathrm{COO}\right)}_2\ \left(\mathrm{aq}\right)+{\mathrm{H}}_2\mathrm{O} $$
(17.1)

Organic acids are well known to be produced as metabolic by-products by various microorganisms, such as Aspergillus niger and Penicillium spp., and numerous studies have been published describing these with a large range of metal sources, both primary and secondary (Anjum et al. 2010; Ilyas et al. 2018).

A key drawback of microbial organic acid producers is that they require an organic carbon source, which adds to both the operating cost and the risk of competing microorganisms. On the positive side, through their local action at the target surface, the biogenic leach reactions can be facilitated without the need for large concentrations of acid in the bulk feed which could be consumed by side reactions with non-target minerals. Thus, metal recovery through this route is of particular interest in the passive treatment of metal-bearing waste materials in heaps (Ilyas et al. 2018).

Biogenic Cyanide

Despite being much maligned for its perceived toxicity, cyanide remains the lixiviant of choice for gold leaching due to its superior properties as a complexing agent, relative stability, and low cost [reaction (17.2)]:

$$ 4\ \mathrm{Au}+8\ \mathrm{NaCN}+{\mathrm{O}}_2+2\ {\mathrm{H}}_2\mathrm{O}\to 4\ {\left[\mathrm{Au}{\left(\mathrm{CN}\right)}_2\right]}^{-}+8\ {\mathrm{Na}}^{+}+4\ {\mathrm{O}\mathrm{H}}^{-} $$
(17.2)

What is often forgotten is that cyanide is produced naturally by many microorganisms and plants, for defence and competitive advantage. Some innovative work has focused on harnessing the cyanide produced by certain microorganisms, in particular Chromobacterium violaceum (Campbell et al. 2001) and Pseudomonas fluorescens (Reith et al. 2007), to directly leach gold from ores, concentrates, and wastes.

A key advantage of generating cyanide in situ is that gold dissolution can be achieved with much smaller concentrations of cyanide than in conventional processes, thus potentially reducing the hazardousness of the leach solution. A major drawback of cyanide-producing organisms is that they generally grow slowly, which limits their usefulness in practical industrial applications (Zammit et al. 2012). The source of nitrogen also impacts the amount of cyanide formed; glycine is typically the best precursor but if other forms of nitrogen are available, cyanide generation tends not to be a preferred reaction (Blumer and Haas 2000). Microorganisms have also found useful application in the biological destruction of cyanide present in waste streams emanating from the mining industry (Zammit et al. 2012).

Iodide-Oxidising Microorganisms

Because of the concerns of the environmental impacts of cyanide, alternative biolixiviants are being explored for gold bioleaching. Kaksonen et al. (2014a) proposed the use of iodide-oxidising microorganisms to regenerate iodide-iodine lixiviant for gold leaching, which has shown considerable promise. Some microorganisms, such as Roseovarius spp. can oxidise I− to I2 with oxygen as the electron acceptor [reaction (17.3); Kaksonen et al. 2014a]:

$$ 4\ {\mathrm{I}}^{-}+{\mathrm{O}}_2+4\ {\mathrm{H}}^{+}\to 2\ {\mathrm{I}}_2+2\ {\mathrm{H}}_2\mathrm{O} $$
(17.3)

Iodide (I−) reacts chemically with iodine (I2) to form triiodide (I3−) according to reaction (17.4); (Kaksonen et al. 2014a):

$$ {\mathrm{I}}^{-}+{\mathrm{I}}_2\to {{\mathrm{I}}_3}^{-} $$
(17.4)

Gold can be solubilised according to reactions (17.5) and (17.6) (Kaksonen et al. 2014a):

$$ 2\ \mathrm{Au}+{{\mathrm{I}}_3}^{-}+{\mathrm{I}}^{-}\to 2\ {\left[{\mathrm{AuI}}_2\right]}^{-} $$
(17.5)
$$ 2\ \mathrm{Au}+{{3\mathrm{I}}_3}^{-}\to 2\ {\left[{\mathrm{AuI}}_4\right]}^{-}+{\mathrm{I}}^{-} $$
(17.6)

Khaing et al. (2019) showed that iodide-oxidising bacteria were able to solubilise gold from sulfidic ore. Further research is needed to explore other applications of iodide-oxidising microorganisms, flow sheet development and optimisation of iodine-based bioleaching processes.

17.4.2 Bio-electrochemical Leaching

The oxidative leaching of sulfide minerals is an electrochemical process, similar to corrosion. Electron transfer is facilitated through a redox intermediary, principally Fe3+/Fe2+ as shown in Fig. 17.1. At the mineral surface electrons are transferred from the mineral (mostly the sulfur species) to the (bio)oxidative reaction system (cathodic reaction) and the mineral dissolves (anodic reaction). The ratio Fe3+/Fe2+, which is linked to the ORP, critically determines the rate of oxidative dissolution at the mineral surface. Whereas the high ORP achieved during bioleaching is desirable for most sulfide minerals, in the case of chalcopyrite, the most common copper mineral, so-called passivation phenomena inhibit the reaction at high ORP, mandating a lower ORP environment (Tanne and Schippers 2017).

A form of ORP control during chalcopyrite bioleaching can be achieved through an electrolysis system in which an anode and a cathode are added to a tank reactor through which current is injected into the solution to facilitate the reduction of excess Fe3+ generated by microbes to Fe2+ thus maintaining the ORP at the desired level. Keeping the ORP at intermediate levels has been found to stimulate microbial growth due to the increased availability of Fe2+ (Natarajan 1992).

A further effect of the added electrolysis system is that direct mineral reduction can take place at the cathode, especially in the context of chalcopyrite reduction to chalcocite, which is much more readily leachable by bioleaching under moderate conditions than the refractory chalcopyrite [reactions (17.7) and (17.8)]:

$$ 2\ {\mathrm{Cu}\mathrm{FeS}}_2+6\ {\mathrm{H}}^{+}+2\ {\mathrm{e}}^{-}\to {\mathrm{Cu}}_2\mathrm{S}+2\ {\mathrm{Fe}}^{2+}+3\ {\mathrm{H}}_2\mathrm{S} $$
(17.7)
$$ {\mathrm{Cu}\mathrm{FeS}}_2+3\ {\mathrm{Cu}}^{2+}+4\ {\mathrm{e}}^{-}\to 2\ {\mathrm{Cu}}_2\mathrm{S}+{\mathrm{Fe}}^{2+} $$
(17.8)

Ahmadi et al. (2011) demonstrated that such a system leaches a chalcopyrite concentrate much more efficiently than bioleaching on its own. Such an electro-assisted bioleaching system may have limited implementation and uptake at large scale, but it remains a promising technique.

17.4.3 Biosorption, Bioaccumulation, and Phytomining

Almost any biomass, living or dead, can act as an adsorbent for soluble metal ions. This is facilitated through the abundance of hydroxyl, carboxyl, amino, and other functional groups at the surface of biomacromolecules which readily form complexes with the metals and thus bind them to the organic phase. Living organisms can adsorb and actively sequester metals within their cell structures, a process referred to as bioaccumulation, as a defence mechanism against metal toxicity (de Freitas et al. 2019). Physical separation of biomass loaded with metals enables their removal from aqueous solution, which makes biosorption and bioaccumulation very appealing in the context of mine wastewater treatment. However, for many types of biomass (cells and macromolecules) easy separation by physical means would require some form of supporting substrate on which the biomass is anchored.

A fundamental concern remains with the subsequent treatment of the loaded biomass to stabilise the sequestered metals so as to prevent their release once the biomass decomposes. Metal recovery from the loaded biomass is therefore a key second step. Metal desorption is usually achieved by treating the loaded biomass with strong acid or base and/or at elevated temperatures to force the adsorbed metals back into aqueous solution, often at elevated concentrations, which allows subsequent recovery through conventional hydrometallurgical techniques. However, while a given biomass may be more selective to certain types of metals than others, biosorption generally shows limited selectivity towards a mixed-metal solution. Therefore, the eluted solution would still require further purification, and the biosorption step can at best be considered an up-concentration of metals from a dilute solution. Another drawback is that the adsorbing biomass tends to become destroyed in the desorption process by the aggressive eluents used, requiring continuous new biomass supply for an ongoing process. Consequently, artificial adsorbents such as ion exchange resins and functionalised porous minerals such as zeolites remain the preferred route for selective and efficient metal removal from aqueous solution. Nonetheless, biosorption remains a feasible option for the passive treatment of metal-containing wastewaters in wetlands and barrier systems with the potential for occasional metal harvesting.

Bioaccumulation of metals in larger plants growing in a metal-rich environment has given rise to the concept of “phytomining”. Certain plant species are known to accumulate metals (often quite selectively) from soils or wetland environments that are abundant in these metals. Examples are Brassicaceae (cruciferous plants), Lamiaceae (herbal plants), and Cunoniaceae, and it is potentially possible to selectively breed and adapt certain plants to maximise their accumulative capacity and selectivity (Sheoran et al. 2009). Such plants can be actively planted and harvested and processed further to extract the accumulated metal value. The harvested plant matter is incinerated or bio-digested, yielding energy and/or useful by-products, whereas the metals are concentrated in the ash/residue to such an extent that they can be directly fed to a conventional process for metal extraction, possibly fuelled by the energy/by-products from the primary step. While again the process is unlikely to find application in primary mining due to its slow pace/large expanse of operations required (phytomining could be perceived as a form of “metal farming”), it is an interesting option for the ameliorating of mine wastewaters in wetlands and in the treatment of contaminated soils.

17.4.4 Biobeneficiation of Minerals

Biobeneficiation of ores through bioflotation and bioflocculation for the separation of valuable minerals from gangue materials have been explored as environmentally friendly alternatives to conventional froth flotation and chemical flocculation. Moreover, bioleaching of impurities, such as phosphorus from ore has been considered as a potential approach to remove penalty elements (Kaksonen et al. 2020). Bioflotation is based on the ability of microbial cells or their metabolites to change the surface properties and hence hydrophobicity or hydrophilicity of minerals. Hydrophobicity increases the floatability of minerals whereas hydrophilicity results in depression of minerals (Behera and Mulaba-Bafubiandi 2017). Bioflocculants are biopolymers which facilitate the agglomeration of fine mineral particles by forming bridges (Kinnunen et al. 2020).

A number of microbial species and their metabolites have been evaluated for their potential for bioflotation and bioflocculation as mineral surface modifiers, activators, depressants, and collectors. The behaviour of microorganisms during bioflotation is influenced by the cell wall and membrane composition and solution pH. The structure and composition of microbial cell walls and membranes differ between archaea and bacteria and between Gram-positive and Gram-negative cells. The composition of cell walls and membranes affects the surface charge and hydrophobicity of the cells. Lipids make cells more hydrophobic resulting in flocculation of cells and adhesion of cells to solids and air bubbles (Behera and Mulaba-Bafubiandi 2017; Kinnunen et al. 2020).

Solution pH affects the surface charge of minerals and microbial cells. Repulsive forces hinder adsorption of cells to minerals when cells and minerals have the same surface charge. Microbial cells are negatively charged when the solution pH is above the microbial isoelectric point (IEP) and positively charged when the pH is below the IEP. Microbial growth substrate, growth phase, culture adaptation, and presence of minerals also influence the surface charge of microbial cells (Kinnunen et al. 2020).

Microbial metabolites evaluated for bioflotation include biosurfactants, proteins, polysaccharides, and nucleic acids. Biosurfactants are surface-active amphiphilic compounds that have both hydrophobic and hydrophilic domains and hence decrease the surface tension of solution and adsorb to mineral surfaces acting as mineral collectors. Single-stranded DNA also has an amphipathic nature with a hydrophilic phosphate backbone and hydrophobic aromatic nitrogenous bases. Polysaccharides present in extracellular polymeric substances (EPS) impart hydrophilicity to mineral surfaces, whereas hydrophobic amino acids of EPS proteins confer hydrophobicity. Iron- and sulfur-oxidising microorganisms can also induce chemical changes to mineral surfaces through biologically catalysed oxidation and reduction processes, which have been utilised, e.g., for pyrite depression (Behera and Mulaba-Bafubiandi 2017). So far bioflotation has only been used in laboratory-scale investigations (Kinnunen et al. 2020). Further research is required for the optimisation of biobeneficiation processes and the evaluation of their techno-economic feasibility.

17.4.5 Upcycling of Metals Through Biomineralisation

Microorganisms are known to play a role in the biogeochemical cycling of metals through biosolubilisation and intra- and extracellular precipitation (Reith et al. 2007). The ability of prokaryotes to precipitate metals, such as sulfides, jarosite, and scorodite, has been utilised in biotechnical mine water and hydrometallurgical water treatment (Kaksonen et al. 2018, 2020). The physicochemical and morphological properties of metals can be improved through biomineralisation and formation of biological nanoparticles (1–100 nm diameter). Metallic nanoparticles have unique antimicrobial, catalytic, electronic, magnetic, and optical properties that can be utilised for a variety of applications, such as catalysis, separation, pharmaceutical, and medical applications (e.g., antibacterial agents, cancer treatment, gene therapy, and targeted drug delivery), imaging (e.g., magnetic resonance imaging and transmission electron microscopy), fuel cells, biosensors, electronics, photonics (e.g., quantum dots) and environmental clean-up (Edmundson et al. 2014; Kaksonen et al. 2020).

The current chemical and physical methods for synthesising metallic nanoparticles typically require high temperatures and/or pressures, and hence are energy intensive and costly. Moreover, the feedstocks for these methods often need to be very pure and are therefore expensive, although biological nanoparticle formation can be carried out at lower temperatures and pressures and with less pure feedstocks, thereby saving costs and enabling the upcycling of metals from waste streams (Edmundson et al. 2014; Kaksonen et al. 2020).

A number of microorganisms have been shown to produce metallic nanoparticles, including both bacteria (e.g., Cupriavidus metallidurans; Cd, Cu, Co, Ge, Ni, Pb, Pd, Y, Zn; Desulfovibrio sp.; Au, Cr, Pd, Pt; Magnetospirillum gryphiswaldense; Fe; Pseudomonas sp.; Ag, Co, Fe, Li, Ni, Pd, Pt, Rh, Ru; Shewanella sp.; Fe), and fungi (e.g. Fusarium oxysporum; Ag, Au, Cd, Pb, Pt, Ti, Zr, and Phoma sp.; Ag; Edmundson et al. 2014). Synthetic biology has been proposed as a tool to functionalise and produce metallic nanoparticles. Through the ability to swap genetic modules in and out of chassis organisms, synthetic biology would allow the production of nanoparticles with various elements and post-production modifications (Edmundson et al. 2014). Further research is required to increase the understanding of and optimise the microbial genetic and metabolic elements that enable biological nanoparticle synthesis (Kaksonen et al. 2020).

17.5 Conclusions

As this concise overview has shown, there are many opportunities for biomining to play a continued, and expanding, role in providing metals for future demand. The exploitation of natural biological processes to this end contributes to a sustainable approach towards metal production, especially if it increasingly includes the recovery of metals from wastes substituting for the large-scale exploitation of primary resources. The optimisation of biomining processes requires consideration of multiple simultaneously occurring chemical, physical, and biological sub-processes. In researching new resources, chemistries, and technologies it is important, therefore, to fully appreciate the techno-economic limitations of bioleaching and judge critically whether, or to what extent, a given approach will yield an industrially feasible solution for the resource of interest in a given context.