Effective bioleaching of low-grade copper ores: Insights from microbial cross experiments

Iron bioleaching and polymers accumulation by an extreme acidophilic bacterium

In many European regions, both local metallic and non-metallic raw materials are poorly exploited due to their low quality and the lack of technologies to increase their economic value. In this context, the development of low cost and eco-friendly approaches, such as bioleaching of metal impurities, is crucial. The acidophilic strain Acidiphilium sp. SJH reduces Fe(III) to Fe(II) by coupling the oxidation of an organic substrate to the reduction of Fe(III) and can therefore be applied in the bioleaching of iron impurities from non-metallic raw materials. In this work, the physiology of Acidiphilium sp. SJH and the reduction of iron impurities from quartz sand and its derivatives have been studied during growth on media supplemented with various carbon sources and under different oxygenation conditions, highlighting that cell physiology and iron reduction are tightly coupled. Although the organism is known to be aerobic, maximum bioleaching performance was obtained by cultures cultivated until the exponential phase of growth under oxygen limitation. Among carbon sources, glucose has been shown to support faster biomass growth, while galactose allowed highest bioleaching. Moreover, Acidiphilium sp. SJH cells can synthesise and accumulate Poly-β-hydroxybutyrate (PHB) during the process, a polymer with relevant application in biotechnology. In summary, this work gives an insight into the physiology of Acidiphilium sp. SJH, able to use different carbon sources and to synthesise a technologically relevant polymer (PHB), while removing metals from sand without the need to introduce modifications in the process set up.

Differential surface modification mechanism of chalcopyrite and pyrite by Thiobacillus ferrooxidans and its response to bioflotation

Mineral processing encounters the challenge of separating chalcopyrite and pyrite, with the conventional high alkali process characterized by issues such as large dosages of reagents, complex procedures, and environmental pollution. This study addresses this challenge by isolating and enriching Thiobacillus ferrooxidans (T·f) from acidic mine drainage, employing it as a biosurfactant. The modification mechanism of T·f was thoroughly analyzed. Fe dissolution through biological oxidation formed a passivation layer (jarosite [KFe3(SO4)2(OH)6], elemental sulfur (S0), and metal sulfides (Cu/Fe-S) on the surface of minerals. Metal oxides, hydroxides, and sulfates were detected on the surface of two minerals, but the difference was that elemental sulfur (S0) and copper sulfide (Cu-S) were detected on the surface of chalcopyrite. elucidating the fundamental reason for the significant difference in surface hydrophobicity between chalcopyrite and pyrite. T·f has been successfully used as a biosurfactant to achieve copper-sulfur separation.

Comparison of bioleaching of a sulfidic copper ore (chalcopyrite) in column percolators and in stirred-tank bioreactors including microbial community analysis

Chalcopyrite is the most abundant Cu-sulfide and economically the most important copper mineral in the world. It is known to be recalcitrant in hydrometallurgical processing and therefore chalcopyrite bioleaching has been thoroughly studied for improvement of processing. In this study, the microbial diversity in 22 samples from the Sarcheshmeh copper mine in Iran was investigated via 16S rRNA gene sequencing. In total, 1063 species were recognized after metagenomic analysis including the ferrous iron- and sulfur-oxidizing acidophilic genera Acidithiobacillus, Leptospirillum, Sulfobacillus and Ferroplasma. Mesophilic as well as moderately thermophilic acidophilic ferrous iron- and sulfur-oxidizing microorganisms were enriched from these samples and bioleaching was studied in shake flask experiments using a chalcopyrite-containing ore sample from the same mine. These enrichment cultures were further used as inoculum for bioleaching experiments in percolation columns for simulating heap bioleaching. Addition of 100 mM NaCl to the bioleaching medium was assessed to improve the dissolution rate of chalcopyrite. For comparison, bioleaching in stirred tank reactors with a defined microbial consortium was carried out as well. While just maximal 32% copper could be extracted in the flask bioleaching experiments, 73% and 76% of copper recovery was recorded after 30 and 10 days bioleaching in columns and bioreactors, respectively. Based on the results, both, the application of moderately thermophilic acidophilic bacteria in stirred tank bioreactors, and natural enrichment cultures of mesoacidophiles, with addition of 100 mM NaCl in column percolators with agglomerated ore allowed for a robust chalcopyrite dissolution and copper recovery from Sarcheshmeh copper ore via bioleaching.

Enhancing column bioleaching of chalcocite by isolated iron metabolism partners Leptospirillum ferriphilum/Acidiphilium sp. coupling with systematically utilizing cellulosic waste

The iron metabolism partners Leptospirillum ferriphilum and Acidiphilium sp. were screened from industrial bioheap site. An integrated multi-stage strategy was proposed to improve chalcolite column bioleaching coupling with synergistical utilization of cellulosic waste such as acid hydrolysate of aquatic plants. L. ferriphilum was used to accelerate the initial iron metabolism, and Acidithiobacillus caldus maintained a lower pH in the middle stage, while Acidiphilium sp. greatly inhibited jarosite passivation in the later stage. Meanwhile, L. ferriphilum (38.3 %) and Acidiphilium sp. (37.0 %) dominated the middle stage, while the abundance of Acidiphilium sp. reached 63.5 % in the later stage. The ferrous, sulfate ion and biomass were improved and the transcriptional levels of some biofilm and morphology related genes were significantly up-regulated. The final Cu2+ concentration reached 325.5 mg·L-1, improved by 43.8 %. Moreover, Canonical Correlation Analysis (CCA) analysis between bioleaching performance, iron/sulfur metabolism and community verified the important role of iron metabolism partners.

Phytoextraction of copper from copper waste rock by Tagetes sp

Due to the ongoing scarcity of copper resources globally, the extraction of copper from waste rocks has become an unavoidable necessity. This study investigated the phytoextraction of copper from low-grade chalcocite (LGC) ore using Tagetes sp. Therefore, the LGC and the garden soil mixtures, with different percentages, were utilized to achieve the optimum condition in 4 weeks. Mixing 50% LGC with 50% soil results in the best uptake value and translocation factor (TF) of 0.42 mg and 1.02, with shoot and root weights of 3.78 and 1.02 g, respectively. However, the highest BCFShoot (bio-concentration factor) and BCFRoot values are 0.65 and 1.66, with shoot and root weights of 2.65 g and 0.5 g, respectively, using 25% LGC + 75% soil. Therefore, at the proportion of 25% of the LGC, it can be concluded that the plant is a moderate accumulator and hyperaccumulator, respectively, for the shoot and root. Both proportions of 25% of the LGC and 50% of the LGC can be selected as optimum conditions for the mixture. If the target is the highest Cu accumulation in the above-ground tissues, the mixture containing 50% LGC should be selected. However, if harvesting the plant roots is possible, the mixture of 25% LGC + 75% soil has a better result because of the highest Cu concentration in the roots. Hence, Tagetes sp. exhibits the capability for extracting copper from low-grade chalcocite.

Copper recovery from low-grade copper sulfides using bioleaching and its community structure succession in the presence of Sargassum

Bioleaching characteristics and bacterial community structure were studied during low-grade copper sulfide ores bioleaching in the presence of pretreated Sargassum (PSM). Results indicated that proportion of attached bacteria and copper recovery were improved by using appropriate-dosage PSM. High copper recovery (82.99%) and low Fe3+ concentration were obtained when 150 mg L-1 PSM was used. Precipitation, such as KFe3(SO4)2(OH)6 and (H3O)Fe3(SO4)2(OH)6, was not found in samples used PSM according to XRD, FTIR and TG analyses, which may result from less passivation layer formed by Fe3+ hydrolysis. I- contained in PSM can act as the reductant to convert Fe3+ into Fe2+, which can reduce Fe3+ hydrolysis and adjust Eh value. Bacterial community structure was influenced significantly by PSM according to the 16 S rDNA analysis. Acidithiobacillus ferrooxidans dominated proportion of bacterial community throughout bioleaching process, whose proportion reached 89.1091% after 14 days in sample added 150 mg L-1 PSM.

Removal of heavy metals from mine tailings by in-situ bioleaching coupled to electrokinetics

This work utilizes a combined biological-electrochemical technique for the in-situ removal of metals from polluted mine tailings. As the main novelty point it is proposed to use electrokinetics (EK) for the in-situ activation of a bioleaching mechanism into the tailings, in order to promote biological dissolution of metal sulphides (Step 1), and for the subsequent removal of leached metals by EK transport out of the tailings (Step 2). Mine tailings were collected from an abandoned Pb/Zn mine located in central-southern Spain. EK-bioleaching experiments were performed under batch mode using a lab scale EK cell. A mixed microbial culture of autochthonous acidophilic bacteria grown from the tailings was used. Direct current with polarity reversal vs alternate current was evaluated in Step 1. In turn, different biological strategies were used: biostimulation, bioaugmentation and the abiotic reference test (EK alone). It was observed that bioleaching activation was very low during Step 1, because it was difficult to maintain acidic pH in the whole soil, but then it worked correctly during Step 2. It was confirmed that microorganisms successfully contributed to the in-situ solubilization of the metal sulphides as final metal removal rates were improved compared to the conventional abiotic EK (best increases of around 40% for Cu, 162% for Pb, 18% for Zn, 13% for Mn, 40% for Ni and 15% for Cr). Alternate current seemed to be the best option. The tailings concentrations of Fe, Al, Cu, Mn, Ni and Pb after treatment comply with regulations, but Pb, Cd and Zn concentrations exceed the maximum values. From the data obtained in this work it has been observed that EK-bioleaching could be feasible, but some upgrades and future work must be done in order to optimize experimental conditions, especially the control of soil pH in acidic values.

Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus

BACKGROUND

The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies.

RESULTS

In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur.

CONCLUSIONS

This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.

Molecular Insights into a Novel Cu(I)-Sensitive ArsR/SmtB Family Repressor in Extremophile Acidithiobacillus caldus

Acidithiobacillus caldus is a common bioleaching bacterium that is inevitably exposed to extreme copper stress in leachates. The ArsR/SmtB family of metalloregulatory repressors regulates homeostasis and resistance in bacteria by specifically responding to metals. Here, we characterized A. caldus Cu(I)-sensitive repressor (AcsR) and gained molecular insights into this new member of the ArsR/SmtB family. Transcriptional analysis indicated that the promoter (PIII) of acsR was highly active in Escherichia coli but inhibited upon AcsR binding to the PIII-acsR region. Size exclusion chromatography and circular dichroism spectra revealed that Cu^I-AcsR shared an identical assembly state with apo-AcsR, as a dimer with fewer α helices, more extended strands, and more β turns. Mutation of the cysteine site in AcsR did not affect its assembly state. Copper(I) titrations revealed that apo-AcsR bound two Cu(I) molecules per monomer in vitro with an average dissociation constant (K_D) for bicinchoninic acid competition of 2.55 × 10^-9 M. Site-directed mutation of putative Cu(I)-binding ligands in AcsR showed that replacing Cys64 with Ala reduces copper binding ability from two Cu(I) molecules per monomer to one, with an average K_D of 6.05 × 10^-9 M. Electrophoretic mobility shift assays revealed that apo-AcsR has high affinity for the 12-2-12 imperfect inverted repeats P2245 and P2270 in the acsR gene cluster and that Cu-loaded AcsR had lower affinity for DNA fragments than apo-AcsR. We developed a hypothetical working model of AcsR to better understand Cu resistance mechanisms in A. caldus. IMPORTANCE Copper (Cu) resistance among various microorganisms is attracting interest. The chemolithoautotrophic bacterium A. caldus, which can tolerate extreme copper stress (≥10 g/L Cu ions), is typically used to bioleach chalcopyrite (CuFeS₂). Understanding of Cu resistance in A. caldus is limited due to scant investigation and the absence of efficient gene manipulation tools. Here, we characterized a new member of the ArsR/SmtB family of prokaryotic metalloregulatory transcriptional proteins that repress operons linked to stress-inducing concentrations of heavy metal ions. This protein can bind two Cu(I) molecules per monomer and negatively regulate its gene cluster. Members of the ArsR/SmtB family have not been investigated in A. caldus until now. The discovery of this novel protein enriches understanding of Cu homeostasis in A. caldus.

Divergent prokaryotic microbial assembly, co-existence patterns and functions in surrounding river sediments of a Cu-polymetallic deposit in Tibet

The exploitation of polymetallic deposits produces large amounts of mine drainage, which poses great challenges to the surrounding aquatic ecosystem. However, the prokaryotic microbial community assembly and co-existence patterns in the polluted area are poorly understood, especially in high-altitude localities. Herein, we investigated the prokaryotic microbial assembly, co-existence patterns and their potential functional responses in surrounding river sediments of a Cu-polymetallic deposit in Tibet. The sediments from mine drainage and surrounding tributaries exhibited distinct geochemical gradients, especially the changes in Cu content. The microbial community structure changed significantly, accompanied by decreased richness and diversity with increased Cu content. Interestingly, the relative abundances of some potential functional bacteria (e.g., Planctomycetota) actually increased as the Cu levels raised. In low contaminated area, ecological drift was the most important assembly process, whereas deterministic processes gained importance with pollution levels. Meanwhile, negative interactions in co-occurrence networks were more frequent with higher modularity and reduced keystone taxa in high contaminated area. Notably, the functions related to ABC transporters and quorum sensing (QS) were more abundant with high Cu content, which helped bacteria work together to cope with the stressful environment. Taken together, the physicochemical gradients dominated by Cu content drove the distribution, assembly and co-existence patterns of microbial communities in surrounding river sediments of a Cu-polymetallic deposit. These findings provide new insights into the maintenance mechanisms of prokaryotic microbial communities in response to heavy metal stress at high altitudes.

A review on the bioleaching of toxic metal(loid)s from contaminated soil: Insight into the mechanism of action and the role of influencing factors

The anthropogenic activities in agriculture, industrialization, mining, and metallurgy combined with the natural weathering of rocks, have led to severe contamination of soils by toxic metal(loid)s. In an attempt to remediate these polluted sites, a plethora of conventional approaches such as Solidification/Stabilization (S/S), soil washing, electrokinetic remediation, and chemical oxidation/reduction have been used for the immobilization and removal of toxic metal(loid)s in the soil. However, these conventional methods are associated with certain limitations. These limitations include high operational costs, high energy demands, post-waste disposal difficulties, and secondary pollution. Bioleaching has proven to be a promising alternative to these conventional approaches in removing toxic metal(loid)s from contaminated soil as it is cost-effective, environmentally friendly, and esthetically pleasing. The bioleaching process is influenced by factors including pH, temperature, oxygen, and carbon dioxide supply, as well as nutrients in the medium. It is crucial to monitor these parameters before and throughout the reaction since a change in any, for instance, pH during the reaction, can alter the microbial activity and, therefore, the rate of metal leaching. However, research on these influencing factors and recent innovations has brought significant progress in bioleaching over the years. This critical review, therefore, presents the current approaches to bioleaching and the mechanisms involved in removing toxic metal(loid)s from contaminated soil. We further examined and discussed the fundamental principles of various influencing factors that necessitate optimization in the bioleaching process. Additionally, the future perspectives on adding omics for bioleaching as an emerging technology are discussed.

Insights into Adaptive Mechanisms of Extreme Acidophiles Based on Quorum Sensing/Quenching-Related Proteins

Quorum sensing (QS) is a unique mechanism for microorganisms to coordinate their activities through intercellular communication, including four main types of autoinducer-1 (AI-1, namely, N-acyl homoserine lactone [AHL]), AI-2, AI-3, and diffusible signaling factor [DSF]) based on signaling molecules. Quorum quenching (QQ) enzymes can disrupt the QS phenomenon by inactivating signaling molecules. QS is proposed to regulate biofilm formation in extremely acidic environments, but the QS/QQ-related genomic features in most acidophilic bacteria are still largely unknown. Here, genome annotation of 83 acidophiles from the genera Acidithiobacillus, Leptospirillum, Sulfobacillus, and Acidiphilium altogether revealed the existence of AI-1, AI-3, DSF, and AhlD (AHL degradation enzyme). The conservative investigation indicated that some QS/QQ-related proteins harbored key residues or motifs, which were necessary for their activities. Phylogenetic analysis showed that LuxI/R (AI-1 synthase/receptor), QseE/F (two-component system of AI-3), and RpfC/G (two-component system of DSF) exhibited similar evolutionary patterns within each pair. Meanwhile, proteins clustered approximately according to the species taxonomy. The widespread Acidithiobacillus strains, especially A. ferrooxidans, processed AI-1, AI-3, and DSF systems as well as the AhlD enzyme, which were favorable for their mutual information exchange and collective regulation of gene expression. Some members of the Sulfobacillus and Acidiphilium without AHL production capacity contained the AhlD enzyme, which may evolve for niche competition, while DSF in Leptospirillum and Acidithiobacillus could potentially combine with the cyclic diguanylate (c-di-GMP) pathway for self-defense and niche protection. This work will shed light on our understanding of the extent of communication networks and adaptive evolution among acidophiles via QS/QQ coping with environmental changes.

IMPORTANCE Understanding cell-cell communication QS is highly relevant for comprehending the regulatory and adaptive mechanisms among acidophiles in extremely acidic ecosystems. Previous studies focused on the existence and functionality of a single QS system in several acidophilic strains. Four representative genera were selected to decipher the distribution and role of QS and QQ integrated with the conservative and evolutionary analysis of related proteins. It was implicated that intra- or intersignaling circuits may work effectively based on different QS types to modulate biofilm formation and energy metabolism among acidophilic microbes. Some individuals could synthesize QQ enzymes for specific QS molecular inactivation to inhibit undesirable acidophile species. This study expanded our knowledge of the fundamental cognition and biological roles underlying the dynamical communication interactions among the coevolving acidophiles and provided a novel perspective for revealing their environmental adaptability.

Microbial recovery of critical metals from secondary sources

The continuous development of technologies involving critical metals, both in Europe and over the world, and geopolitical challenges in areas rich in critical metal sources, imposed increased research efforts to recover them from secondary sources, by eco-efficient processes. Yet, microbes-metal interactions are not sufficiently exploited to recover metals from secondary sources, although they are already used in ore extraction. This review examines and compare strategies and processes involving microorganisms for critical metals recovery, since conventional physico-chemical methods are energy-intensive and often polluting. Two groups of microbial assisted recovery processes are discussed: metal mobilization from metal bearing waste, and selective metal separation from leaching solutions by immobilization on microbial biomass. Because most of the identified microbial technologies are developed on laboratory scale, the increase of biorecovery efficiency is compulsory for enhancing scaling-up potential. Future developments focused on novel microorganisms and high-performance strategies for critical metal recovery by microbial processes are considered.

Copper and Zinc Recovery from Sulfide Concentrate by Novel Artificial Microbial Community

Exploring efficient methods to enhance leaching efficiency is critical for bioleaching technology to deal with sulfide concentrate. In our study, a novel artificial microbial community was established to augment the bioleaching efficiency and recovery of copper (Cu) and zinc (Zn). The optimum parameters in bioleaching experiments were explored according to compare a series of conditions from gradient experiments: the pH value was 1.2, temperature was 45 °C, and rotation speed was 160 r/min, which were different with pure microorganism growth conditions. Under optimal conditions, the result of recovery for Cu and Zn indicated that the average leaching rate reached to 80% and 100% respectively, which almost increased 1.8 times and 1.2 times more than control (aseptic condition) group. Therefore, this method of Cu and Zn recovery using a new-type artificial microbial community is expected to be an environmentally-friendly and efficient bioleaching technology solution, which has the potential of large-field engineering application in the future.

An Old Technique with A Promising Future: Recent Advances in the Use of Electrodeposition for Metal Recovery

Although the first published works on electrodeposition dates from more than one century ago (1905), the uses of this technique in the recovery of metals are attracting an increasing interest from the scientific community in the recent years. Moreover, the intense use of metals in electronics and the necessity to assure a second life of these devices in a context of circular economy, have increased the interest of the scientific community on electrodeposition, with almost 3000 works published per year nowadays. In this review, we aim to revise the most relevant and recent publications in the application of electrodeposition for metal recovery. These contributions have been classified into four main groups of approaches: (1) treatment and reuse of wastewater; (2) use of ionic liquids; (3) use of bio-electrochemical processes (microbial fuel cells and microbial electrolysis cells) and (4) integration of electrodeposition with other processes (bioleaching, adsorption, membrane processes, etc.). This would increase the awareness about the importance of the technology and would serve as a starting point for anyone that aims to start working in the field.

Hazardous minerals mining: Challenges and solutions

Minerals are valuable resources gifted to man from the Mother Earth and quite often they need to be dug out from deep down with much effort to utilize them in many of our anthropogenic activities. The fascinating nature, colours as well as the physicochemical properties of minerals has extended their prospective value in the synthesis of various household and industrial products. However, knowledge of the mostly explored minerals, associated products, and their hazardous nature becomes relevant to its prevalence in our daily life. The harmful effects of some minerals are mostly evident from its site of occurrence, process of mining, post mining wastes left over and even in finished products. The current review focuses to evaluate the hazardous nature of minerals, cautions associated with its mining, drastic effects on human health, and ecosystem as an eye-opener to us. Finally, the effective remedies that could be implemented in the exploration of minerals are also discussed to the best of our knowledge. Bioleaching methods of rare earth elements and copper have been discussed briefly to explain the pros and cons of biological methods over conventional chemical leaching methods.

An integrated insight into bioleaching performance of chalcopyrite mediated by microbial factors: Functional types and biodiversity

Six artificial communities with different function or biodiversity were reconstructed by six typical bioleaching species for chalcopyrite leaching. Absence of sulfur oxidizers in communities significantly reduced copper extraction rates, and low diversity communities also exhibited slightly poor bioleaching performances. The variations of pH, redox potential, ferrous and copper ions indicated that the community with both sulfur oxidizers and high diversity showed fast adaptation to the environment and rapid dissolution of chalcopyrite. Integrated analysis of mineralogical and microbial parameters demonstrated that functional types of microorganisms made more contributions in mediating chalcopyrite dissolution than microbial diversity. Further correlation analysis between microbial types and chalcopyrite dissolution performances showed that sulfur oxidizers, especially Acidithiobacillus caldus, could greatly accelerate chalcopyrite dissolution by regulating solution physicochemical factors, such as redox potential and pH. This study provided a theoretical basis for improving bioleaching efficiency by balancing microbial functional types and biodiversity.

Mechanical Activation on Bioleaching of Chalcopyrite: A New Insight

Mechanical activation as a means of accelerating the mineral dissolution may play an important role in chalcopyrite bioleaching. In the present work, the mechanical activation by ball-milling with 10 min, 30 min, 60 min, 90 min, 120 min and 180 min time periods of bioleaching of chalcopyrite was studied, and then evaluated by a Density Functional Theory (DFT) calculation. The results showed that the specific surface area increased sharply in the very beginning of mechanical activation and then increased slowly until the agglomeration of the particles occurred, while the chalcopyrite lattices increased with the mechanical activation. The reaction activity analyzed by cyclic voltammetry (CV) increased slowly in 30 min, increased quickly in the following 90 min, and then decreased, while the hydrophobicity analyzed by contact angles of the chalcopyrite after activation showed less of a change. The results showed that after 15 days of bioleaching, the Cu leaching by Sulfobacillus thermosulfidooxidans (S. thermosulfidooxidans) increased from 9.39% in the 0 min of mechanical activation to 87.41% in the 120 min of mechanical activation, and the copper leaching rate increased by about 78%. The DFT results provide solid proof that the activated chalcopyrite can be adsorbed more easily by cells with higher adsorption energies and stronger bonds.