Keywords

9.1 Development and Current Status of Copper Bioleaching in Chile

Although Chile has been considered a mineral-rich territory since colonial times, its copper mining industry only started to grow at the beginning of the twentieth century, transforming the country’s economy. Since these early years, several new technologies such as from the early process of vat percolation leaching, electrowinning (EW), and copper cementation to, in the 1970s, solvent extraction (SX), “thin layer” (TL) bioleaching processes (1980s) which use mostly mineral layers of 0.5–1 m (greater in some cases), and chloride copper leaching (2000s) have been adapted concomitantly, in parallel with several changes in the copper industry (Domic 2007, Gentina and Acevedo 2016).

The combination of TL-SX-EW technology in Chile started by the technological developments achieved at Lo Aguirre mine, Minera Pudahuel, which was located close to Santiago. In 1975, the company decided to apply thin layer heap bioleaching, previously patented by Holmes and Narver (H & N) in California (US patent number 4017309A). Improvements of the TL process, led to its application in 1980, concomitantly with a second patent for the process in 1981. In addition to its applicability for copper oxides, the TL process allowed secondary copper sulfides, such as chalcocite, covellite, and bornite to be processed. Microbial oxidative action on ores increased both the concentration of ferric iron (the main metal sulfide-oxidising agent), and the oxidation of sulfur and reduced inorganic sulfur compounds (RISCs), ensuring the acidic pH required by mineral-oxidising acidophilic prokaryotes. The ore initially contained mainly copper oxides, but over the years, a growing proportion of the feed consisted of chalcocite (Cu2S). A nominal 15,000 t y−1 of copper cathodes was produced from the time of start-up until the site was shut down in 2001 due to the total depletion of the deposit (Domic 2001).

A very positive scenario for the expansion of biohydrometallurgical projects occurred during the 1990s, fuelled by a combination of several factors such as rising copper prices, depletion of higher-grade ores, increment of costs, and environmental concerns. These, together with an increase of foreign investment in Chile, led to significant changes in the implementation of new projects for copper recovery. Several projects based on the more environmentally friendly TL-SX-EW processes started, leading to production of high-quality copper cathodes at competitive costs. The development of TL-SX-EW copper cathode production in Chile since 1990 is shown in Fig. 9.1. Rapid expansion occurred during 1995–2010, and production of 2088 kt of SX-EW copper cathodes was obtained in 2010. During that period, bioleaching also attracted interest and reached a significant level of maturity. By 2010, out of the 2088 kt of total TL-SX-EW copper production, the Chilean copper bioleaching production contribution was 556 kt per year, led by the Minera Escondida, Minera Spence, Chuquicamata, and Quebrada Blanca operations.

Fig. 9.1
figure 1

Total production of copper cathodes in kt per year, by TL-SW-EW in Chile between 1990 and 2020. Adapted from Cochilco Annual Statistics Report, 2020 (https://www.cochilco.cl/Paginas/Estadisticas/Publicaciones/Anuario.aspx)

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By 2012, bioleaching became the standard method for low-grade copper sulfide processing, allowing processing of copper feed grades as low as 0.4%. Table 9.1 shows a benchmark of the main operations by 2012 (Enrique Roman, personal communication). This table includes different types of processes, among these Lo Aguirre, Carmen Andacollo, and Spence used permanent heaps, while Quebrada Blanca, Cerro Colorado, and Zaldívar used “on-off” heap leaching (intermittent irrigation), the latter with run-of-mine (ROM) material. Other operations also including ROM material were Escondida, Los Bronces, and Chuquicamata. It is interesting to note that the latter was the first investment in hydrometallurgy operations made by the Chilean state-owned company, Codelco, which applied dump leaching to ROM ore with low recovery (<25%) of copper. The SX–EW units began operations in mid-1994, with a design production level of 12,500 t y−1 of copper cathodes (Domic 2007). During this time, the feasibility of applying bioleaching at a new mine (Ministro Hales), with ores rich in arsenic sulfides, was studied by a joint venture between Codelco and BHP Billiton, using the high temperature BioCop™ sulfide concentrate leaching technology. The process employed thermophilic microorganisms in agitation tanks, operating at temperatures between 65 and 80 °C. A benefit of the copper dissolution was the possibility of precipitating and removing soluble arsenic as inert scorodite (FeAsO4), which is highly stable in aerobic environments. At the time, the operational costs were much higher than those associated with conventional concentrate smelting and refining, and the joint venture ended. BHP sold its part of the pilot plant facility to Codelco, who transformed the industrial facility into Ecometales (www.ecometales.cl), a subsidiary dedicated to the treatment of solution impurities, particularly arsenic by chemical oxidation followed by generation of scorodite.

The Quebrada Blanca operation is situated at an altitude of 4000 m above sea level. It was the first TL process application on a chalcocite ore body, containing about 1% total copper. The plant started in 1994 with a designed capacity of 75,000 t y−1 of copper cathode, and by 2012 it had reached 80,000 t y−1, exceeding the designed production. Since the oxides and secondary sulfides were almost completely mined out, the annual production dropped to 21,100 t y−1 in 2019. Quebrada Blanca is currently switching to production of copper concentrates, with a projected 28-year life-of-mine expansion, by the installation of a 140,000 t day−1 concentrator mill plant, to produce 316,000 t y−1 of copper.

The Zaldívar mine is located in the Antofagasta region of Chile and operations there started in mid-1995, reaching a maximum production of 150,000 t y−1 of copper cathode in 2002, which fell to 116,000 t y−1 by 2019. By early 2021, the Zaldívar mine operation had switched to chloride leaching to reduce cycle times and improve copper recovery.

The Escondida operation belongs to an international consortium composed of BHP Billiton (57.5%), Rio Tinto (30%), Mitsubishi (10%) and International Finance Corporation (2.5%). In addition to the production of copper concentrates for direct export, Escondida also produces copper cathodes via TL–SX–EW operation. Copper sulfides are mainly composed of low-grade chalcocite and covellite (Table 9.1). Due to the increment in primary sulfide proportion, the process has recently switched to chloride leaching.

Table 9.1 Benchmarking between bioleaching operations, 2012 (Roman E, personal communication)
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Spence is operated exclusively by BHP, and has produced copper cathodes by microbial leaching. The deposit contains reserves of copper oxides (1.14% Cu, mainly as atacamite; Cu2Cl(OH)3) and copper sulfide ores (1.12% Cu, primarily supergene chalcocite and some minor amounts of covellite; CuS). These are mined and processed separately, as atacamite generates solutions that are rich in chloride, and oxides leach about twice as fast as the sulfides (Domic 2007). The sulfide ore fraction contains chalcocite, covellite, and chalcopyrite.

Within the last 10 years, Chile has been facing a serious change in the exploitation of its copper ore reserves. The production of copper by TL-SX-EW has decreased, due to the depletion of copper oxides and secondary sulfide ores, as well as a decline in their copper grades, leading to a significant amount of idle SX-EW capacity (Lagos et al. 2018). Despite previously being widely accepted, the long operational cycles and low recoveries associated with bioleaching of ROM have become of increasing concern. In addition, some companies have switched their operations to leaching with high chloride-containing solutions. Projections indicate that the amount of copper production by heap leaching will decrease from a current (2020/2021) estimate of ~30% to approximately 10% by 2027. Concomitant with this decline in heap (bio)leaching, production of copper concentrates will increase to around 90%, with a very small increase in the total amount of copper produced per year (Cochilco 2017).

A comparison of the state of the most prominent bioleaching operations in 2009 and 2019 is shown in Table 9.2. Current main operations using biohydrometallurgy include Cerro Colorado, Quebrada Blanca, Escondida, Zaldívar, and Spence. The Cerro Colorado operation is located in the Antofagasta region, and commenced in 1993, with a starting production capacity of 45 kt y−1 of copper cathodes. By 2013, Cerro Colorado reached a total annual copper production of 130 kt y−1. Since then, the annual production has declined until reaching current levels of 70 kt y−1. The environmental permits are expected to expire in 2023, and therefore a down-scaling process has begun. In 2016, under the control of BHP, the operation switched to a full chloride leaching process, to improve secondary sulfide ore leaching kinetics and copper recovery.

Table 9.2 Major bioleaching operations in Chile: production comparison between 2009 and 2019
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Codelco, at the Radomiro Tomic division, has been applying the BioSigma process (see Sect. 9.2.1), for almost a decade. The first industrial test was performed between 2012 and 2014, by using two pilot heaps of 25.000 t of ore each. Biomass was produced in an external bioreactor, which was periodically removed and directly inoculated into the leaching solution and the heap. Usually, the copper ore grade is less than 0.4% and more than 70% consisted of primary copper sulfides, mainly bornite and chalcopyrite. The testing facility has been used to design the ROM bioleaching process at Radomiro Tomic operation, which will allow production of 10,000 t y−1 of copper, with an estimated recovery of 25% Cu.

Another project currently applying bioleaching is the Sociedad Punta del Cobre (Pucobre), located in the Atacama region. This mine started operations in 1989, with a copper mill concentrator and since 1993 has operated a bioleaching process. Sulfide ore is mined from the 3.5 Mt. y−1 Punta del Cobre underground mine and transported 5 km for its treatment at San Jose plant. The plant is located 18.5 km from Copiapó. Today, the plant can produce over 110,000 t y−1 of copper concentrates, grading ~29% copper. In recent years, bioleaching operations have been focused in copper concentrates, reaching 75 t y−1 of cathodes production using bioleaching technology (Pucobre team, personal communication).

The most prominent events that have occurred in Chile in relation to the implementation of the TL-SX-EW, applied to copper, are listed in Table 9.3.

Table 9.3 Prominent events in the implementation of the TL-SX-EW technology in Chile (updated from Domic 2007)
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9.2 Research, Development, and Biomining Applications in Chile: Industrial Cases

Over the past 30–35 years, there has been a major contribution made by universities in Chile in devising and communicating the results of research projects with potential application to mineral bioprocessing. Some of these projects developed in partnership with large and medium-sized mining companies have generated some interesting results, though these have often faced problems with follow through. The continuous structural changes that the mining industry in Chile faces have had major impact on the application of new technologies, as their continuity is affected by management decisions primarily responding to short-term economics. This has resulted in a shortening of time for long-term development of technologies, with consequent impairment to show their ultimate potential. Nevertheless, at least two companies have significantly contributed to advances in the development and application of bioleaching in Chile, as described below.

9.2.1 BioSigma-CodelcoTech

In 2002, the BioSigma company was launched as a joint venture between the mining companies Codelco (Chile) and JX Nippon Mining and Metals (Japan). The main aim of BioSigma was to commercialise comprehensive biotechnological solutions for sustainable mining, with a commitment to open innovation in Chile and worldwide. At the beginning of 2017, BioSigma was merged with other technological subsidiaries from Codelco, under the name of CodelcoTech, a subsidiary finally closed in 2020 due to corporate decisions. At its peak (2012) BioSigma employed about 100 personnel that had a multidisciplinary profile with its highly qualified technical and professional staff qualified in different specialties. During its 15 years of operation, BioSigma achieved important scientific and technological advances, such as isolating different microorganisms and selecting microbial consortia with improved action and differentiated activities such as oxidation of iron and/or elemental sulfur and inorganic sulfur compounds. This included microbial consortia with greater resistance to cations and anions typically present in elevated concentrations in mining solutions, with a concomitant improved action on chalcopyrite ores. Additionally, from sequencing and annotation of the genomes of isolated microorganisms and the use of high-performance technologies such as transcriptomics, proteomics, and metabolomics, it was possible to establish databases on the genes, proteins and metabolites that participate in the process of bioleaching of copper sulfide mineralogical species, with the corresponding development of biomarkers, the understanding of the importance of certain nutrients and the negative effect produced by certain toxic compounds inherent to the operation process (Bobadilla-Fazzini et al. 2014, 2017; Martínez et al. 2013, 2015). All of this allowed a comprehensive analysis of bioleaching processes, and to develop and patent different analysis and prediction tools, such as phenomenological models of bioleaching heap operation and bioreactor performance, as well as the design of efficient biomass production systems, with the correct microbial activity necessary for the process (US patent number US7837760B2). The latter was reflected in the construction of a pilot biomass plant at the Radomiro Tomic division. This plant was planned to reach a potential operation for inoculating 7.2 Mt. of mineral y−1. It is also worth mentioning the importance of the development of bio-characterisation technologies for the in situ monitoring of the bioleaching process. For this, several technologies were adapted over time, from Denaturing Gradient Gel Electrophoresis (DGGE), through PCR, qPCR, DNA microarrays, up to the use of cutting-edge technologies, such as massively parallel sequencing (NGS) and Q-TOF mass spectrometry. All of this fundamental science development, involving different universities, technology centres and companies, generated relevant information that allowed progress for scaling-up bioleaching of primary copper sulfides in heaps. In addition, the foundations for an improved biomining process, specifically to achieve significant copper recoveries from low-grade sulfides, were established. In 2005, results of laboratory studies initiated validation tests in pilot-scale bioleaching operations using 2500 ton heaps of sulfide minerals located in the Chuquicamata division, Codelco Norte. In 2007, along with continuing the pilot works to validate its technology at the Codelco Norte Division, BioSigma began the industrial prototype validation in 50,000 t heaps containing low-grade primary sulfide mineral at the Andina division (Region de Valparaíso, Los Andes). In this process, the first copper cathodes were obtained with BioSigma’s technology (Codelco 2007). Continuing with the scaling and validation on an industrial scale of the BioSigma bioleaching process under actual operating conditions, an industrial-scale plant to produce bioleaching microorganisms for heap inoculation was constructed, and began operation towards the end of 2010, in the Radomiro Tomic division (Codelco 2009). With this capability, an industrial test of crushed ore and ROM material in heaps was carried out between 2012 and 2014 with the application of BioSigma inoculation technology, using consortia of acidophilic microorganisms, and compared with conventional acid treatment leaching technologies. The results were encouraging, with copper recoveries between 30% and 50% greater than competing technologies, and achieved within in a much shorter period of time. With these positive results, Codelco, at Radomiro Tomic division decided to integrate BioSigma bioleaching technology into its production plans during the second half of 2014. This first project was designed to treat 3.6 Mt. of low-grade sulfur ROM ore. The planned amount was increased to 5 Mt. of low-grade mineral for the year 2015 (Codelco 2014). Additionally, a patent related to a solid-phase inoculation technology, “BioSigma Bioleaching Seeds” (BBS; Patent number US10131961B2), that enhanced the BioSigma liquid inoculation technology by improving homogeneous inoculation of the ore, greater microbial resistance to potential toxins and elevated solute potentials, and improved cell viability during manipulation, transport, and storage of the microorganisms, was developed. The BBS technology was combined with an integrated biofilter or “BioSigma Bioleaching Filter” (BBF; INAPI applicant number 201903901), which allowed the use of direct high toxic process solutions (raffinate) with a low fresh water consumption. This conferred several advantages to the inoculation process, such as providing protection of microorganisms against high ionic loads, reduction of biomass volume, possibility for long-term storage, safe transport as well as ensuring a more homogeneous inoculation process (Martínez and Parada 2013).

At the start of 2017, the fusion of three Codelco technological subsidiaries, including BioSigma, resulted in the formation of CodelcoTech. Its main aim was to continue with development of technologies promoted by the former subsidiaries, integrating them under the wing of the current Codelco’s corporate roadmap. The remaining BioSigma personnel, now under CodelcoTech, continued to work on technologies (referred to as “2.0”), by facing the challenge of promoting already validated technologies but adapting them to current scenarios. These included problems such as water scarcity, new environmental regulations, and changes in mining operations. Major efforts were focused on technologies for increasing the efficiency of bioleaching through conjugated and sequential processes with oxidants, such as chloride leaching, and the development of mobile modular reactors with higher performance and lower investment costs, among others. Additionally, new lines of development for bioleaching and biotechnology were opened. Among these, the feasibility of exploiting secondary resources such as tailings represents a potentially enormously valuable resource, considering the huge amount of tailings deposits in Chile (over 750 tailing dumps, Sernageomin, https://www.sernageomin.cl/datos-publicos-deposito-de-relaves). In this context, the extraction capacity through bioleaching of critical elements for international industry, such as rare earth elements (REE), nickel, cobalt, among others has gained increasing attention. In addition, there are challenges in physically and chemically stabilising these environmental mining liabilities, bearing in mind their potential use in other industrial applications such as construction. Bioleaching applications have opened an opportunity to use a sustainable circular economy model that can help develop a new way of mining. The CodelcoTech team directed a national project that tackled all these issues with interesting results for the recovery of valuable elements, such as cobalt, using bioleaching technologies, between 2017 and 2020. In parallel, thanks to collaboration with universities and technology centres, other mining issues related with treatment of sulfate-laden waters and acid mine drainage were addressed, through biotreatment in reactors and directed microbiological control (Schwarz et al. 2020; Suárez et al. 2020).

In 2020, the decision was made to close CodelcoTech, with the consequent freezing of all technological developments initiated by BioSigma and continued by the CodelcoTech team. Even so, at the Radomiro Tomic division, the biomass plant referred to above continues to operate, being integral to the optimisation stage to feed mineral to be treated by bioleaching.

The BioSigma-CodelcoTech case in Chile was associated with development and use of bioleaching of low-grade primary sulfides, mainly in large-scale mining (copper production of between 100,000–500,000 t y−1), as was the case of Codelco. It is also interesting to mention that there are other private efforts, where advances have been made in biotechnological developments aimed at medium-sized mining (copper production of less than 50,000 t y−1). In these cases, this type of disruptive technologies may have a greater opportunity of being integrated into the process and developed over time.

9.2.2 Pucobre: LIAP

Another interesting case is LIAP, a translated acronym for “Applied Research Laboratory”, a company born as a spin-off of the mining company Pucobre, a medium-sized mining company located in the Atacama region, which has been in operation for more than 30 years. LIAP was created in 2011 under the challenge of using bioleaching technology to extract copper at the Biocobre cathode plant, near the city of Copiapó. This challenge generated the development of a laboratory with capabilities to develop technology. It has also allowed tackling some other challenges such the treatment of complex concentrates, a topic that is currently of cross-cutting interest in Chilean mining industry. Many mining sites contain arsenic minerals, and copper concentrates containing arsenic are penalised in their commercialisation in the international market, and cannot be processed pyrometallurgically, due to current regulations. These developments have allowed the company to develop patented technologies, such as the Biocobre technology (US patent 10036081B2), that allows bioleaching of concentrates and tailings material agglomerated with plastic, in a circular economy model that includes waste from different industries. Currently, LIAP-Pucobre is completing a bioleaching pilot program with this technology in confined heaps with 300 t of complex concentrates with high arsenic content. Recoveries of over 90% of copper and other metals, such as gold and silver, have been reported within in a period of operation of 200 days (LIAP team, personal communication).

9.3 Conclusions and Future of Bioleaching in Chile

Chile, as the largest global copper producing-country, faces the need to advance in the generation of more sustainable and environmentally friendly mining methods, to contribute to the construction of a new economy that takes into account the challenges faced by humanity. In this regard, the international community is demanding the use of latest-generation tools and new ways of mining. While Chile’s potential in mining production, particularly with copper, has remained relatively intact over time, conditions enabling the development of the mining industry are changing at both national and global scales.

Copper extraction is becoming every year more difficult and energy demanding. The decline in the quality of the geological resources, specifically the decrease in copper grades of current ore deposits, has created a scenario under which mining companies must make great efforts to maintain their current production levels (Lagos et al. 2018). The factors influencing the downturn in productivity include, among others, long haulage distances due to the deepening of ore reservoirs requiring increased movement of ore material. The deterioration of ore quality requires also more complex processing schemes, due to the greater hardness of the rock and the presence of more complex mineralogy and complex contaminants. In addition, the depletion of copper oxides has generated surplus capacity at SX-EW plants, which leads to an opportunity for the processing of complex and low-grade sulfide minerals through hydrometallurgy to fill this capacity, including other metals as cobalt. All these factors are stimulating the need for a strong development of innovative and sustainable technologies to ensure copper production compatible with environmental regulations.

The exponential advances experienced in biotechnology within the last 40 years have captured the attention of the mining industry, in order to explore how to solve some of the above-mentioned challenges. Chile, as a mining country, has been generating knowledge in the last 35 years applied to the development of bioleaching. Although some of the private research and development initiatives have not continued due to multiple factors, the knowledge and progress achieved so far could form the basis for new discoveries and developments to be applied in the near future at new Chilean mining projects. Future mining will target the processing of secondary resources, such as tailings and gravel as well as ROM, and it is increasingly positioning bioleaching as a natural solution perfectly compatible with social demands of sustainability.

One of the keys for the application of innovative technologies that have less impact on global ecosystems, such as bioleaching and other applications in mining associated with applied biotechnology, has been R&D performed mainly in technology centres, universities and mining companies. The latter have played an important role in Chile, although applied research projects have not been without problems, especially with regard to their long-term continuity. As has been observed during the last two decades, these initiatives have been affected by how metal mining is carried out in Chile. Clearly there is a need to promote future changes in project development and planning, so that not only production variables but also sustainability variables are taken into consideration when devising future R&D projects in biomining. Although taking into account the setbacks described, bioleaching shows several advantages compared to other technologies that guarantee its application in some specific areas, and a significant growth could be achieved if R&D is scheduled to fill the current gaps in years to come. For instance, it is well-accepted that bioleaching has a lower cost over alternatives in the treatment of very low-grade sulfidic ores, especially ROM. This economical advantage makes feasible the economical extraction of marginal copper grade ore and therefore increases the mining reserves. Therefore its application with this kind of material is a natural niche to continue its development. Another application of bioleaching may focus on the re-processing of fresh or abandoned tailings, as it allows valorisation of current environmental liabilities. This approach links with circular economy and zero mining waste policies, giving the mining industry an important seal of sustainability, not only in the case of copper, but also for other critical elements for world industry, such as REE, cobalt, nickel, magnesium, and others. Another bioleaching area of current interest is the treatment of complex concentrates that contain appreciable amounts of toxic elements, such as arsenic, which currently either cannot be processed by smelters or are sold to markets with significant economical penalties. Bioleaching could make feasible the economical production of copper-enriched liquors, leaving behind the contaminants, with the additional potential to use the idle capacity of many Chilean SX-EW plants. Finally, the search for synergies between bacterial activity and alternative chemical leaching technologies, such as chloride leaching, has become of great interest to develop more effective and efficient solutions for particularly challenging ores.