Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A

Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching

The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REEs). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole-genome knockout collection for the bioleaching microbe Gluconobacter oxydans B58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in extraction by up to 111% (δGO_1598, disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δGO_1096, disruption of the gene encoding the GTP-binding protein TypA). Notable changes in pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching by G. oxydans through genetic engineering.

The invisible architects: microbial communities and their transformative role in soil health and global climate changes

During the last decades, substantial advancements have been made in identifying soil characteristics that impact the composition of the soil microbiome. However, the impacts of microorganisms on their respective soil habitats have received less attention, with the majority of prior research focusing on the contributions of microbes to the dynamics of soil carbon and nitrogen. Soil microbiome plays a critical role in soil habitats by influencing soil fertility, crop yields, and biotic and abiotic stress tolerance. In addition to their roles in nutrient cycling and organic matter transformations, soil microorganisms affect the soil environment via many biochemical and biophysical mechanisms. For instance, the soil microbiome plays an essential role in soil mechanical stability and pore connectivity and regulates the flow of nutrients, oxygen, and water. Similarly, soil microbiomes perform various critical functions in an ecosystem, which leads to carbon stabilization for a long time and could serve as microbiome engineering targets for global climate change mitigation. In this review, considering soil structure, hydrology, and chemistry, we outline how microorganisms alter the soil ecosystem. Further, this study investigates the mechanisms by which feedback loops can be generated between microorganisms and soil. Moreover, we analyze the potential of microbially mediated modifications of soil properties as a viable strategy to address soil threats and global climate challenges. In addition, the current study propose a deep learning-based approach to develop a synthetic microbial consortium to improve soil health and mitigate climate change.

Study on the Extraction of Rare Earth Elements (REEs) from Phosphogypsum Using Gluconobacter oxydans Culture Solution

With the rapid development of modern industry, particularly in the fields of electric vehicles and renewable energy technologies, the demand for rare earth elements (REEs) has surged dramatically. Phosphogypsum (PG), which is an industrial waste product generated during the production of phosphoric acid through the sulfuric acid process, is rich in REEs. However, traditional chemical leaching methods pose environmental pollution and resource wastage issues. This study aims to explore the feasibility and optimal conditions for bioleaching REEs from phosphogypsum using Gluconobacter oxydans (G. oxydans). The phase composition and components of phosphogypsum, as well as the growth characteristics and leaching efficiency of G. oxydans, were analyzed in detail using SEM, EDS, XRD, and XRF techniques. Experimental results indicate that G. oxydans can effectively leach REEs from phosphogypsum under conditions of 28 °C, an agitation speed of 150 rpm, and a liquid-to-solid ratio of 4:1, with a maximum leaching efficiency of 24.67%. Moreover, it is revealed in the study that G. oxydans exhibits selectivity in leaching REEs. Specifically, the leaching efficiency for Nd is significantly enhanced at low pH values. This research provides a theoretical basis and practical application example for the efficient and environmentally friendly recovery of REEs from phosphogypsum.

Bacterial biofilm-based bioleaching: Sustainable mitigation and potential management of e-waste pollution

Significant advances in the electrical and electronic industries have increased the use of electrical and electronic equipment and its environmental emissions. The e-waste landfill disposal has deleterious consequences on human health and environmental sustainability, either directly or indirectly. E-waste containing ferrous and non-ferrous materials can harm the surrounding aquatic and terrestrial environments. Therefore, recycling e-waste and recovering metals from it before landfill disposal is an important part of environmental management. Although various chemical and physical processes are being used predominantly to recover metals from e-waste, the bioleaching process has gained popularity in recent years due to its eco-friendliness and cost-effectiveness. Direct contact between microbes and e-waste is crucial for continuous metal dissolution in the bio-leaching process. Biofilm formation is key for the continuous dissolution of metals from e-waste in contact bioleaching. Critical reviews on microbial activities and their interaction mechanisms on e-waste during metal bioleaching are scarce. Therefore, this review aims to explore the advantages and disadvantages of biofilm formation in contact bioleaching and the practical challenges in regulating them. In this review, sources of e-waste, available metallurgical methods, bioleaching process, and types of bioleaching microbes are summarized. In addition, the significance of biofilm formation in contact bioleaching and the role and correlation between EPS production, cyanide production, and quorum sensing in the biofilm are discussed for continuous metal dissolution. The review reveals that regulation of quorum sensing by exogenous and endogenous processes facilitates biofilm formation, leading to continuous metal dissolution in contact bioleaching.

Extremophilic Microorganisms as a Source of Emerging Enzymes for the Food Industry: A Review

Modern-day consumers are interested in highly nutritious and safe foods with corresponding organoleptic qualities. Such foods are increasingly subjected to various processing techniques which include the use of enzymes. These enzymes like amylases, lipases, proteases, xylanases, laccases, pullulanase, chitinases, pectinases, esterases, isomerases, and dehydrogenases could be derived from extremophilic organisms such as thermophiles, psychrophiles, acidophiles, alkaliphiles, and halophiles. As these organisms can grow under severe environmental conditions, they can produce functional enzymes (extremozymes) used in producing safe foods (such as gluten-free, lactose-free, lower acrylamide, or lower trans-fat products). The extremozymes also enhance nutrient bioavailability and bioaccessibility (e.g., predigested nourishments like baby formulae), and improve nourishment functionalities such as surface, sensory, and bioactive properties. Therefore, exploring alternative sources of enzymes for better compatibility and long-term adaptability in the processing stages is a promising approach for obtaining novel food products. This review will establish novel discovery methods of extremozymes from psychrophiles, thermophiles, acidophiles, alkaliphiles, and halophiles, the enzymes' types, mechanisms of action, and their food applications. It will also contribute to their commercial relevance and the furtherance of their discovery.

Recent advances in bioleaching and biosorption of metals from waste printed circuit boards: A review

Electronic waste, commonly known as "e-waste", refers to electrical or electronic equipment that has been discarded. E-waste, especially waste-printed circuit boards (WPCBs), must be handled carefully; as they can cause serious environmental pollution and threaten the health of local residents. The most abundant metal in WPCBs is copper, in addition to gold, aluminum, nickel, and lead, with grades that are tens or even hundreds of times higher than those of natural deposits. Due to the superiority of biorecovery methods in terms of their environmental friendliness, low capital investment and low operating costs, this study focuses on recent advances in the bioleaching and biosorption of metals from WPCBs. First, the principles, methods, and efficiency of bioleaching are reviewed in detail, particularly acidolysis, redoxolysis, and complexolysis. Additionally, six major factors (microbes, pH, temperature, nutrients, aeration, and substrate) affecting bioleaching are analyzed. The principles, kinetics, and isotherms of biosorption are then reviewed, and the factors influencing biosorption, including temperature and pH, are elaborated on. Hybrid recovery with biorecovery is explored, as these integrated strategies are conducive to achieving selective and efficient metal recovery. Finally, we discuss the advantages and disadvantages of the bioleaching and biosorption processes for metal recovery from WPCBs, particularly in terms of recovery efficiency, recovery time, and cost. Furthermore, future developments in biorecovery are also examined, along with useful ideas on how to accomplish energy-efficient metal recovery from WPCBs in the future.

Bioleaching of rare earth elements from ores and waste materials: Current status, economic viability and future prospects

Rare earth elements (REEs) are critical components of numerous products widely used in many areas, and the demand for REEs is increasing dramatically in recent years. Physical-chemical leaching is commonly adopted for the recovery of REEs from ores and solid wastes, but concerns over the generation of hazards, operation safety, and environmental pollution have urged the transition to greener and more sustainable leaching methods. Bioleaching is considered an excellent alternative for the recovery of REEs. This review provided an overview on the REEs recovery from primary and secondary resources via different bioleaching strategies. The techno-economics of bioleaching for REEs recovery were highlighted, and key factors affecting the economic viability of bioleaching were identified. Finally, strategies including the utilization of low-cost substrates as feedstocks, non-sterile bioleaching, recycling and reutilization of biolixiviants, and development of robust bioleaching strains were proposed to improve the economic competitiveness of bioleaching. It is expected that this review could serve as a useful guideline on the design of more economically competitive bioleaching processes for the recovery REEs from different resources.

Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities

Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.

Unveiling the Bioleaching Versatility of Acidithiobacillus ferrooxidans

Acidithiobacillus ferrooxidans is a Gram-negative bacterium that thrives in extreme acidic conditions. It has emerged as a key player in biomining and bioleaching technologies thanks to its unique ability to mobilize a wide spectrum of elements, such as Li, P, V, Cr, Fe, Ni, Cu, Zn, Ga, As, Mo, W, Pb, U, and its role in ferrous iron oxidation and reduction. A. ferrooxidans catalyzes the extraction of elements by generating iron (III) ions in oxic conditions, which are able to react with metal sulfides. This review explores the bacterium's versatility in metal and elemental mobilization, with a focus on the mechanisms involved, encompassing its role in the recovery of industrially relevant elements from ores. The application of biomining technologies leveraging the bacterium's natural capabilities not only enhances element recovery efficiency, but also reduces reliance on conventional energy-intensive methods, aligning with the global trend towards more sustainable mining practices. However, its use in biometallurgical applications poses environmental issues through its effect on the pH levels in bioleaching systems, which produce acid mine drainage in rivers and lakes adjacent to mines. This dual effect underscores its potential to shape the future of responsible mining practices, including potentially in space, and highlights the importance of monitoring acidic releases in the environment.

Bioleaching of lithium from jadarite, spodumene, and lepidolite using Acidiothiobacillus ferrooxidans

Lithium (Li) is becoming increasingly important due to its use in clean technologies that are required for the transition to net zero. Although acidophilic bioleaching has been used to recover metals from a wide range of deposits, its potential to recover Li has not yet been fully explored. In this study, we used a model Fe(II)- and S-oxidising bacterium, Acidiothiobacillus ferrooxidans (At. Ferrooxidans), to extract Li from three different minerals and kinetic modelling to predict the dominant reaction pathways for Li release. Bioleaching of Li from the aluminosilicate minerals lepidolite (K(Li,Al)3(Al,Si,Rb)4O10(F,OH)2) and spodumene (LiAl(Si2O6)) was slow, with only up to 14% (approximately 12 mg/L) of Li released over 30 days. By contrast, At. ferrooxidans accelerated Li leaching from a Li-bearing borosilicate clay (jadarite, LiNaB3SiO7OH) by over 50% (over 120 mg/L) in 21 days of leaching, and consistently enhanced Li release throughout the experiment compared to the uninoculated control. Biofilm formation and flocculation of sediment occurred exclusively in the experiments with At. ferrooxidans and jadarite. Fe(II) present in the jadarite-bearing clay acted as an electron donor. Chemical leaching of Li from jadarite using H2SO4 was most effective, releasing approximately 75% (180 mg/L) of Li, but required more acid than bioleaching for pH control. Kinetic modelling was unable to replicate the data for jadarite bioleaching after primary abiotic leaching stages, suggesting additional processes beyond chemical leaching were responsible for the release of Li. A new crystalline phase, tentatively identified as boric acid, was observed to form after acid leaching of jadarite. Overall, the results demonstrate the potential for acidophilic bioleaching to recover Li from jadarite, with relevance for other Li-bearing deposits.

Biotechnological Approaches for Metal Recovery from Electronic Wastes

The disposal of electronic waste (EW) in open landfills has caused several toxic environmental effects. The harmful metallic components released in the environment due to deposition of EW act as hazards for living systems. EW management has been widely studied in recent days across the world. Though, several processes are implemented in extraction, recycling and recovery of heavy metals from the EW, most of them are not effective in recovering the precious metals. Various chemical processes are executed for efficient extraction of precious metals from e-wastes. Though the techniques are easy to process and rapid, however, the chemical leaching also has detrimental environmental consequences. Biological approaches, on the other hand, solves the purpose for efficient and environmentally friendly recovery of precious metals. Thus, both resource recovery as well as remediation can be targeted simultaneously. Biotechnological methods offer sustainable and efficient solutions for metal recovery from electronic wastes, presenting a viable alternative to traditional methods. Continued advancements in this field hold significant promise for addressing the growing e-waste challenge.

Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing

Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.

Architectural Decoration of Bioleached NiFeP Surfaces by Co3O4 Flowers for Efficient Electrocatalytic Hydrogen Generation

In the quest for sustainable hydrogen production via water electrolysis, the development of high-performance, noble-metal-free catalytic systems is highly desired. Herein, we proposed an innovative strategy for the development of an electrocatalyst by refining the surface characteristics of a NiFeP alloy through microbiological techniques and subsequent enrichment of active sites by tailoring 3D hierarchical flower-like structures with intact and interconnected two-dimensional (2D) Co3O4. The resultant 3D Co3O4@NiFeP-5/24h has a porous structure comprised of intercrossed nanoparticles covering the entirety of the catalytic surface. This design ensures comprehensive electrolyte ion penetration and facilitates the release of gas bubbles while reducing bubble adhesion rates. Remarkably, the Co3O4@NiFeP-5/24h electrode demonstrates superior hydrogen evolution (HER) performance in an alkaline medium, characterized by its high stability, low overpotential (106 mV at a current density of 10 mA cm-2), and reduced Tafel slope (98 mV dec-1). Besides, the minimized interfacial contact resistance among the phases of electrode and electrolyte emphasizes the high HER performance of the 3D Co3O4@NiFeP-5/24h electrode. The innovative design and fabrication strategy employed herein holds significant potential for advancing the field of water-splitting electrocatalysis, offering a promising path toward the rational design and development of noble-metal-free electrocatalysts.

Harnessing the potential of the microbial sulfur cycle for environmental biotechnology

The sulfur cycle is a complex biogeochemical cycle characterized by the high variability in the oxidation states of sulfur. While sulfur is essential for life processes, certain sulfur compounds, such as hydrogen sulfide, are toxic to all life forms. Micro-organisms facilitate the sulfur cycle, playing a prominent role even in extreme environments, such as soda lakes, acid mine drainage sites, hot springs, and other harsh habitats. The activity of these micro-organisms presents unique opportunities for mitigating sulfur-based pollution and enhancing the recovery of sulfur and metals. This review highlights the application of sulfur-oxidizing and -reducing micro-organisms in environmental biotechnology through three illustrative examples. Additionally, it discusses the challenges, recent trends, and prospects associated with these applications.

A novel closed-loop biotechnology for recovery of cobalt from a lithium-ion battery active cathode material

In recent years, the demand for lithium-ion batteries (LIBs) has been increasing rapidly. Conventional recycling strategies (based on pyro- and hydrometallurgy) are damaging for the environment and more sustainable methods need to be developed. Bioleaching is a promising environmentally friendly approach that uses microorganisms to solubilize metals. However, a bioleaching-based technology has not yet been applied to recover valuable metals from waste LIBs on an industrial scale. A series of experiments was performed to improve metal recovery rates from an active cathode material (LiCoO2; LCO). (i) Direct bioleaching of ≤0.5 % LCO with two prokaryotic acidophilic consortia achieved >80 % Co and 90 % Li extraction. Significantly lower metal recovery rates were obtained at 30 °C than at 45 °C. (ii) In contrast, during direct bioleaching of 3 % LCO with consortia adapted to elevated LCO levels, the 30 °C consortium performed significantly better than the 45 °C consortium, solubilizing 73 and 93 % of the Co and Li, respectively, during one-step bioleaching, and 83 and 99 % of the Co and Li, respectively, during a two-step process. (iii) The adapted 30°C consortium was used for indirect leaching in a low-waste closed-loop system (with 10 % LCO). The process involved generation of sulfuric acid in an acid-generating bioreactor (AGB), 2-3 week leaching of LCO with the biogenic acid (pH 0.9), selective precipitation of Co as hydroxide, and recirculation of the metal-free liquor back into the AGB. In total, 58.2 % Co and 100 % Li were solubilized in seven phases, and >99.9 % of the dissolved Co was recovered after each phase as a high-purity Co hydroxide. Additionally, Co nanoparticles were generated from the obtained Co-rich leachates, using Desulfovibrio alaskensis, and Co electrowinning was optimized as an alternative recovery technique, yielding high recovery rates (91.1 and 73.6% on carbon felt and roughened steel, respectively) from bioleachates that contained significantly lower Co concentrations than industrial hydrometallurgical liquors. The closed-loop system was highly dominated by the mixotrophic archaeon Ferroplasma and sulfur-oxidizing bacteria Acidithiobacillus caldus and Acidithiobacillus thiooxidans. The developed system achieved high metal recovery rates and provided high-purity solid products suitable for a battery supply chain, while minimizing waste production and the inhibitory effects of elevated concentrations of dissolved metals on the leaching prokaryotes. The system is suitable for scale-up applications and has the potential to be adapted to different battery chemistries.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress

Extreme acidophilic bacteria like Leptospirillum sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of Leptospirillum sp. CF-1 encodes the thioredoxin-fold protein TFP2, which exhibits a high structural similarity to the thioredoxin domain of E. coli CnoX. CnoX from Escherichia coli is a chaperedoxin that protects protein substrates from oxidative stress conditions using its holdase function and a subsequent transfer to foldase chaperones for refolding. Recombinantly produced and purified Leptospirillum sp. TFP2 possesses both thioredoxin and chaperone holdase activities in vitro. It can be reduced by thioredoxin reductase (TrxR). The tfp2 gene co-locates with genes for the chaperone foldase GroES/EL on the chromosome. The "tfp2 cluster" (ctpA-groES-groEL-hyp-tfp2-recN) was found between 1.9 and 8.8-fold transcriptionally up-regulated in response to 1 mM hydrogen peroxide (H2O2). Leptospirillum sp. tfp2 heterologously expressed in E. coli wild type and cnoX mutant strains lead to an increased tolerance of these E. coli strains to H2O2 and significantly reduced intracellular protein aggregates. Finally, a proteomic analysis of protein aggregates produced in E. coli upon exposition to oxidative stress with 4 mM H2O2, showed that Leptospirillum sp. tfp2 expression caused a significant decrease in the aggregation of 124 proteins belonging to fifteen different metabolic categories. These included several known substrates of DnaK and GroEL/ES. These findings demonstrate that Leptospirillum sp. TFP2 is a chaperedoxin-like protein, acting as a key player in the control of cellular proteostasis under highly oxidative conditions that prevail in extreme acidic environments.

Factors affecting the adoption of circular economy in mining companies of developing economies - A Namibian stakeholder perspective

The factors influencing the adoption and implementation of CE in developing countries are not yet fully examined. By focusing on the Namibian mining sector, this study highlights the perspectives of local stakeholders on CE adoption in a developing country. The mine managers recognized that waste is problematic and that CE practices are beneficial for mining companies and Namibia at large. Our findings also indicated that stronger academic institutions providing CE training and helping develop CE solutions, public awareness campaigns, financial support for CE practices, cooperation among industry stakeholders, and clear CE policy would all help drive the implementation of CE.

Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms

Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.

Goethite dissolution by acidophilic bacteria

Previous studies have reported the role of some species of acidophilic bacteria in accelerating the dissolution of goethite under aerobic and anaerobic conditions. This has relevance for environments impacted by acid mine drainage and for the potential bioleaching of limonitic laterite ores. In this study, natural well-characterized goethite mineral samples and synthetic goethite were used in aerobic and anaerobic laboratory batch culture incubation experiments with ferric iron-reducing, acidophilic bacteria, including the lithoautotrophic species Acidithiobacillus (At.) thiooxidans, At. ferrooxidans, and At. caldus, as well as two strains of the organoheterotrophic species Acidiphilium cryptum. All bacteria remained alive throughout the experiments and efficiently reduced soluble ferric iron in solution in positive control assays. However, goethite dissolution was low to negligible in all experimental assays with natural goethite, while some dissolution occurred with synthetic goethite in agreement with previous publications. The results indicate that ferric iron-reducing microbial activity at low pH is less relevant for goethite dissolution than the oxidation of elemental sulfur to sulfuric acid. Microbial ferric iron reduction enhances but does not initiate goethite dissolution in very acidic liquors.

Do ferrous iron-oxidizing acidophiles (Leptospirillum spp.) disturb aerobic bioleaching of laterite ores by sulfur-oxidizing acidophiles (Acidithiobacillus spp.)?

The extraction of nickel, cobalt, and other metals from laterite ores via bioleaching with sulfur-oxidizing and ferric iron-reducing, autotrophic, acidophilic bacteria (e.g. Acidithiobacillus species) has been demonstrated under anaerobic as well as aerobic conditions in experiments in different laboratories. This study demonstrated the bioleaching of laterites from Brazil with the addition of elemental sulfur in 2-L stirred-tank bioreactors with pure and mixed cultures of Acidithiobacillus and Sulfobacillus species under aerobic conditions. In particular, a potential disturbance of mineral dissolution under aerobic conditions by ferrous iron-oxidizing acidophiles likely introduced as contaminants in an applied bioleaching process was investigated with Leptospirillum ferrooxidans at 30°C and Leptospirillum ferriphilum at 40°C, at maintained pH 1.5 or without maintained pH leading to an increase in acidity (with pH values <1.0) due to the biological production of sulfuric acid. Despite the proportion of ferrous iron to the total amount of extracted iron in the solution being drastically reduced in the presence of Leptospirillum species, there was a negligible effect on the extraction efficiency of nickel and cobalt, which is positive news for laterite bioleaching under aerobic conditions.

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.

Metal recovery from spent lithium-ion batteries via two-step bioleaching using adapted chemolithotrophs from an acidic mine pit lake

The demand for lithium-ion batteries (LIBs) has dramatically increased in recent years due to their application in various electronic devices and electric vehicles (EVs). Great amount of LIB waste is generated, most of which ends up in landfills. LIB wastes contain substantial amounts of critical metals (such as Li, Co, Ni, Mn, and Cu) and can therefore serve as valuable secondary sources of these metals. Metal recovery from the black mass (shredded spent LIBs) can be achieved via bioleaching, a microbiology-based technology that is considered to be environmentally friendly, due to its lower costs and energy consumption compared to conventional pyrometallurgy or hydrometallurgy. However, the growth and metabolism of bioleaching microorganisms can be inhibited by dissolved metals. In this study, the indigenous acidophilic chemolithotrophs in a sediment from a highly acidic and metal-contaminated mine pit lake were enriched in a selective medium containing iron, sulfur, or both electron donors. The enriched culture with the highest growth and oxidation rate and the lowest microbial diversity (dominated by Acidithiobacillus and Alicyclobacillus spp. utilizing both electron donors) was then gradually adapted to increasing concentrations of Li+, Co2+, Ni2+, Mn2+, and Cu2+. Finally, up to 100% recovery rates of Li, Co, Ni, Mn, and Al were achieved via two-step bioleaching using the adapted culture, resulting in more effective metal extraction compared to bioleaching with a non-adapted culture and abiotic control.

Bioleaching of polymetallic sulphidic mining residues: influence of increasing solid concentration on microbial community dynamics and metal dissolution

Within the European research project NEMO, a bioleaching strategy was developed for efficient metal extraction from bioleach residue currently heap-leached at Sotkamo (Finland) that still contains sulphidic minerals and valuable metals (Ni, Zn, Co, Cu). The strategy of gradually increasing the solid content with 5% steps allowed the adaptation of the consortium up to 20% (w/w) solid content, with efficient metal dissolution and same dominant bacteria. Largest proportions of Sulfobacillusthermosulfidooxidans while Eh increased suggested it to be most involved in iron oxidation. Acidithiobacilluscaldus was rather found when pH stabilized, in line with a production of protons from sulphur oxidation that maintained low pH. 'Acidithiomicrobium' P2 was favoured towards the end of the runs and at 20% (w/w) solids possibly due to its tolerance to Ni. The use of gene abundance to evaluate biomass in the pulp provided complementary results to classical cell counts in the liquid phase, and suggested a key role of bacteria associated to mineral particles in iron oxidation. Scaling-up in 21-L stirred-tank reactor at 20% (w/w) solids had no detrimental effect on bioleaching and confirmed metal extraction rates. 'Acidithiomicrobium' P2 and Sb. thermosulfidooxidans remained main actors. However, the biological activity was considerably reduced at 30% (w/w) solid concentration, which may be due to a too drastic environmental change for the bacteria to adapt to higher solid concentration. Efficient bioleaching of Sotkamo bioleaching residue at high solid concentration was demonstrated, as well as the robustness of the selected moderately thermophilic consortium, at laboratory and pilot scales.

Rates of iron(III) reduction coupled to elemental sulfur or tetrathionate oxidation by acidophilic microorganisms and detection of sulfur intermediates

Bioleaching processes and acid mine drainage (AMD) generation are mainly driven by aerobic microbial iron(II) and inorganic sulfur/compound oxidation. Dissimilatory iron(III) reduction coupled to sulfur/compound oxidation (DIRSO) by acidophilic microorganisms has been described for anaerobic cultures, but iron reduction was observed under aerobic conditions as well. Aim of this study was to explore reaction rates and mechanisms of this process. Cell-specific iron(III) reduction rates for different Acidithiobacillus (At.) strains during batch culture growth or stationary phase with iron(III) (∼40 mM) as electron acceptor and elemental sulfur or tetrathionate as electron donor (1% or 5 mM, respectively) were determined. The rates were highest under anaerobic conditions for the At. ferrooxidans type strain with 6.8 × 106 and 1.1 × 107 reduced iron(III) ions per second per cell for growth on elemental sulfur and tetrathionate, respectively. The iron(III) reduction rates were somehow lower for the anaerobically sulfur grown archaeon Ferroplasma acidiphilum, and lowest for the sulfur grown At. caldus type strain under aerobic conditions (1.7 × 106 and 7.3 × 104 reduced iron(III) ions per second per cell, respectively). The rates for five strains of At. thiooxidans (aerobe) were in between those for At. ferrooxidans (anaerobe) and At. caldus (aerobe). There was no pronounced pH dependence of iron(III) reduction rates in the range of pH 1.0-1.9 for the type strains of all species but rates increased with increasing pH for four other At. thiooxidans strains. Thiosulfate as sulfur intermediate was found for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III) but not during anaerobic growths on elemental sulfur and iron(III), and a small concentration was measured during aerobic growths on tetrathionate without iron(III). For the At. thiooxidans type strain thiosulfate was found with tetrathionate grown cells under aerobic conditions in presence and absence of iron(III), but not with sulfur grown cells. Evidence for hydrogen sulfide production at low pH was found for the At. ferrooxidans as well as the At. thiooxidans type strains during microaerophilic growth on elemental sulfur and for At. ferrooxidans during anaerobic growths on tetrathionate and iron(III). The occurrence of sulfur compound intermediates supports the hypothesis that chemical reduction of iron(III) ions takes place by sulfur compounds released by the microbial cells.

Bioleaching of metals from spent fluid catalytic cracking catalyst using adapted Acidithiobacillus caldus

In this study, an adapted bioleaching strain of Acidithiobacillus caldus UVS10 was successfully developed. Batch tests and tests in bioreactor were conducted to evaluate the metals bioleaching performance of A. caldus UVS10 to spent FCC catalyst (SFCCC). Results of batch experiments showed the bioleaching efficiency of Ni, V, La, and Ce in SFCCC reached 19.40%, 22.06%, 53.75%, and 59.56%, respectively. High SFCCC pulp density inhibited the leaching of metals. Sb leaching was inhibited in acidic environment caused by A. caldus UVS10. Contents of Ni, V, La, and Ce in extracellular polymeric substances (EPS) were significantly higher than those intracellular. Accumulation of metal in EPS and cytosol increased with the increase of SFCCC pulp density. V was less intercepted by EPS than Ni, La, and Ce, because of lower toxicity. Experimental results in bioreactor showed that Ni, V, La, and Ce could be effectively leached by A. caldus UVS10 under 10% pulp density. The aeration and stirring operating environment in bioreactor improved the leaching efficiency of metals in SFCCC. After bioleached in bioreactor, the available fraction content of four metals in SFCCC decreased significantly. Ecological risk analysis demonstrated the environmental risks of bioleached SFCCC were significantly lower than raw SFCCC. Different reaction kinetic models were used to represent metals leaching behavior under bioleaching of A. caldus UVS10, leaching of La and Ce showed good agreement with the product layer diffusion model, while Ni and V leaching kinetics fit well with the surface chemical reaction models.

Bioleaching of heavy metals from metal tailings utilizing bacteria and fungi: Mechanisms, strengthen measures, and development prospect

Recovering key metals from secondary sources is an indispensable strategy for preventing metal shortages and reducing the risk of toxic releases into the environment. Metal mineral resources continue to be depleted and the global supply chain will face metal scarcity. The use of microorganisms for metal transformation plays an important role in the bioremediation of secondary resources. It shows great potential for development due to its compatibility with the environment and possible cost effectiveness. The results of the study show that the influence of bioleaching processes and effects are mainly analyzed from microorganisms, mineral properties and leaching environmental conditions. In this review article, we elucidate light on the role and mechanisms of fungi and bacteria involved in extracting different metals from tailings, including acidolysis, complexolysis, redoxolysis, and bioaccumulation. Key process parameters that affect the efficiency based bioleaching are discussed, providing referenceable pathways to improve leaching efficiency. The investigation concludes that exploitation of the functional genetic role of microorganisms and their optimal growth conditions can achieve efficient leaching of metals. It was found that the improvement of microbial performance was achieved at the level of mutagenesis breeding, mixed culture microorganisms, and genetics. Moreover, control of leaching system parameters and removal of passivation films can be achieved by adding biochar and surfactants in the leaching system as an effective means to improve tailings leaching. Knowledge about cells with minerals and their detailed interactions at the molecular level is still relatively scarce and the field could be deepened and this area needs to be further explored in the future. The challenges and the key issues associated with the bioleaching technology development are elaborated as a green and effective bioremediation strategy for the environment and prospects for imminent are also highlighted.

Comparative genomics of the proteostasis network in extreme acidophiles

Extreme acidophiles thrive in harsh environments characterized by acidic pH, high concentrations of dissolved metals and high osmolarity. Most of these microorganisms are chemolithoautotrophs that obtain energy from low redox potential sources, such as the oxidation of ferrous ions. Under these conditions, the mechanisms that maintain homeostasis of proteins (proteostasis), as the main organic components of the cells, are of utmost importance. Thus, the analysis of protein chaperones is critical for understanding how these organisms deal with proteostasis under such environmental conditions. In this work, using a bioinformatics approach, we performed a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems. The analysis included 35 genomes from iron- or sulfur-oxidizing autotrophic, heterotrophic, and mixotrophic acidophilic bacteria. The results showed that classical ATP-dependent chaperones, mostly folding chaperones, are widely distributed, although they are sub-represented in some groups. Acidophilic bacteria showed redundancy of genes coding for the ATP-independent holdase chaperones RidA and Hsp20. In addition, a systematically high redundancy of genes encoding periplasmic chaperones like HtrA and YidC was also detected. In the same way, the proteolytic ATPase complexes ClpPX and Lon presented redundancy and broad distribution. The presence of genes that encoded protein variants was noticeable. In addition, genes for chaperones and protease systems were clustered within the genomes, suggesting common regulation of these activities. Finally, some genes were differentially distributed between bacteria as a function of the autotrophic or heterotrophic character of their metabolism. These results suggest that acidophiles possess an abundant and flexible proteostasis network that protects proteins in organisms living in energy-limiting and extreme environmental conditions. Therefore, our results provide a means for understanding the diversity and significance of proteostasis mechanisms in extreme acidophilic bacteria.

Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms

Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

Kappa-carrageenan for benign preparation of CdSeNPs enhancing the electrochemical measurement of AC symmetric supercapacitor device based on neutral aqueous electrolyte

This study presents the development of an electrochemical supercapacitor with a cadmium selenide nanoparticles (CdSeNPs) electrode utilizing a straightforward and economical method based on kappa-carrageenan (κ-CGN). The structural, morphological, and optical characteristics of CdSeNPs were assessed. Activated carbon (AC) and green-prepared CdSeNPs were easily mixed to achieve excellent electrochemical properties. The nanoelectrode (AC@CdSe) was tested in an aqueous electrolyte of sodium sulfate (Na₂SO₄) with a concentration of 1 Molar. Specific capacitance (Csp) for the AC electrode and the AC@CdSe electrode at 1 A g^-1 was calculated to be 103 and 480 F g^-1, respectively. Besides, the symmetric supercapacitor AC@CdSe/AC@CdSe device has a high specific energy of 52 Wh kg^-1 and a maximum specific power of 2880 W kg^-1, with a specific capacitance of 115.5 F g^-1. With a coulombic efficiency of between 82 % and 100 %, the device continues to maintain excellent capacitance after 10.000 cycles.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH &lt; 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.