Microbiological Advances in Biohydrometallurgy

Simulating compatible solute biosynthesis using a metabolic flux model of the biomining acidophile, Acidithiobacillus ferrooxidans ATCC 23270

Halotolerant, acidophilic, bioleaching microorganisms are crucial to biomining operations that utilize saline water. Compatible solutes play an important role in the adaptation of these microorganisms to saline environments. Acidithiobacillus ferrooxidans ATCC 23270, an iron- and sulfur-oxidizing acidophilic bacterium, synthesizes trehalose as its native compatible solute but is still sensitive to salinity. Recently, halotolerant bioleaching bacteria were found to use ectoine as their key compatible solute. Previously, bioleaching bacteria were recalcitrant to genetic manipulation; however, recent advancements in genetic tools and techniques allow successful genetic modification of A. ferrooxidans ATCC 23270. Therefore, this study aimed to test, in silico, the effect of native and synthetic compatible solute biosynthesis by A. ferrooxidans ATCC 23270 on its growth and metabolism. Metabolic network flux modelling was used to provide a computational framework for the prediction of metabolic fluxes during production of native and synthetic compatible solutes by A. ferrooxidans ATCC 23270, in silico. Complete pathways for trehalose biosynthesis by the bacterium are proposed and captured in the updated metabolic model including a newly discovered UDP-dependent trehalose synthesis pathway. Finally, the effect of nitrogen sources on compatible solute production was simulated and showed that using nitrogen gas as the sole nitrogen source enables the ectoine-producing 'engineered' microbe to oxidize up to 20% more ferrous iron in comparison to the native microbe that only produces trehalose. Therefore, the predictive outcomes of the model have the potential to guide the design and optimization of a halotolerant strain of A. ferrooxidans ATCC 23270 for saline bioleaching operations.

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.

Examining the Osmotic Response of Acidihalobacter aeolianus after Exposure to Salt Stress

Acidihalobacter aeolianus is an acidophilic, halo-tolerant organism isolated from a marine environment near a hydrothermal vent, an ecosystem whereby levels of salinity and total dissolved salts are constantly fluctuating creating ongoing cellular stresses. In order to survive these continuing changes, the synthesis of compatible solutes—also known as organic osmolytes—is suspected to occur, aiding in minimising the overall impact of environmental instability. Previous studies on A. aeolianus identified genes necessary for the accumulation of proline, betaine and ectoine, which are known to act as compatible solutes in other halophilic species. In this study, the impact of increasing the osmotic stress as well as the toxic ion effect was investigated by subjecting A. aeolianus to concentrations of NaCl and MgSO₄ up to 1.27 M. Exposure to high concentrations of Cl⁻ resulted in the increase of ectC expression in log-phase cells with a corresponding accumulation of ectoine at stationary phase. Osmotic stress via MgSO₄ exposure did not trigger the same up-regulation of ectC or accumulation of ectoine, indicating the transcriptionally regulated response against osmotic stress was induced by chloride toxicity. These findings have highlighted how the adaptive properties of halo-tolerant organisms in acidic environments are likely to differ and are dependent on the initial stressor.

Enabling Circular Economy: The Overlooked Role of Inorganic Materials Chemistry

Circular economy is considered a new chance to build a more sustainable world from both the social and the economic point of view. In this Essay, the possible contribution of inorganic chemistry towards a smooth transition to circularity in inorganic materials design and production is discussed by adopting an interdisciplinary approach.

RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite

Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.

Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov

The genus Acidihalobacter has three validated species, Acidihalobacter ferrooxydans, Acidihalobacter prosperus and Acidihalobacter aeolinanus, all of which were isolated from Vulcano island, Italy. They are obligately chemolithotrophic, aerobic, acidophilic and halophilic in nature and use either ferrous iron or reduced sulphur as electron donors. Recently, a novel strain was isolated from an acidic, saline drain in the Yilgarn region of Western Australia. Strain F5T has an absolute requirement for sodium chloride (>5 mM) and is osmophilic, growing in elevated concentrations (>1 M) of magnesium sulphate. A defining feature of its physiology is its ability to catalyse the oxidative dissolution of the most abundant copper mineral, chalcopyrite, suggesting a potential role in biomining. Originally categorized as a strain of A. prosperus, 16S rRNA gene phylogeny and multiprotein phylogenies derived from clusters of orthologous proteins (COGS) of ribosomal protein families and universal protein families unambiguously demonstrate that strain F5T forms a well-supported separate branch as a sister clade to A. prosperus and is clearly distinguishable from A. ferrooxydans DSM 14175T and A. aeolinanus DSM14174T. Results of comparisons between strain F5T and the other Acidihalobacter species, using genome-based average nucleotide identity, average amino acid identity, correlation indices of tetra-nucleotide signatures (Tetra) and genome-to-genome distance (digital DNA-DNA hybridization), support the contention that strain F5T represents a novel species of the genus Acidihalobacter. It is proposed that strain F5T should be formally reclassified as Acidihalobacter yilgarnenesis F5T (=DSM 105917T=JCM 32255T).

Identification of a gene encoding a novel thiosulfate:quinone oxidoreductase in marine Acidithiobacillus sp. strain SH

Sulfur-oxidizing bacteria that are halophilic and acidophilic have gained interest because of their potential use in bioleaching operations in salt-containing environments. Acidithiobacillus sp. strain SH, which was previously identified as Acidithiobacillus thiooxidans based on its 16S rRNA gene sequence, is a chemolithoautotrophic marine bacterium exhibiting sodium chloride-stimulated thiosulfate-oxidizing activities. A novel thiosulfate:quinone oxidoreductase from strain SH (SH-TQO) has been purified from its solubilized membrane fraction. The gene for SH-TQO was determined from the draft genome sequence of the strain SH. Amino acid sequences of peptides generated by the in-gel trypsin digestion of SH-TQO were found in a protein encoded by locus tag B1757_09800 of the genome of the strain SH. The gene encoded 444 amino acids with a signal peptide of 29 amino acids and was annotated to encode a porin. The gene was located in a unique genomic region, not found in A. thiooxidans strains, suggesting that the strain SH acquired this region through a horizontal gene transfer. A protein-protein basic local alignment search revealed that sulfur-oxidizing bacteria, such as Acidithiobacillus species have proteins homologous to SH-TQO, though the degree of homologies was relatively low. The protein, DoxXA, which is homologous to TQO from Acidianus amvibalens, was also found in the genomic region.

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia

Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30 °C and 48 °C, but not 42 °C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48 °C endogenous consortium (80%), then the 42 °C exogenous BRGM-KCC consortium (71%), and finally the 30 °C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48 °C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.

Bioleaching of Phosphate Minerals Using Aspergillus niger: Recovery of Copper and Rare Earth Elements

Rare earth elements (REE) are essential in high-technology and environmental applications, where their importance and demand have grown enormously over the past decades. Many lanthanide and actinide minerals in nature are phosphates. Minerals like monazite occur in small concentrations in common rocks that resist weathering. Turquoise is a hydrous phosphate of copper and aluminum scarcely studied as copper ore. Phosphate-solubilizing microorganisms are able to transform insoluble phosphate into a more soluble form which directly and/or indirectly contributes to their metabolism. In this study, bioleaching of heavy metals from phosphate minerals by using the fungus Aspergillus niger was investigated. Bioleaching experiments were examined in batch cultures with different mineral phosphates: aluminum phosphate (commercial), turquoise, and monazite (natural minerals). The experiments were performed at 1% pulp density and the phosphorous leaching yield was aluminum phosphate > turquoise > monazite. Bioleaching experiments with turquoise showed that A. niger was able to reach 8.81 mg/l of copper in the aqueous phase. Furthermore, the fungus dissolved the aluminum cerium phosphate hydroxide in monazite, reaching up to 1.37 mg/L of REE when the fungus was grown with the mineral as the sole phosphorous source. Furthermore, A. niger is involved in the formation of secondary minerals, such as copper and REE oxalates.

Distinct Roles of Acidophiles in Complete Oxidation of High-Sulfur Ferric Leach Product of Zinc Sulfide Concentrate

A two-step process, which involved ferric leaching with biologically generated solution and subsequent biooxidation with the microbial community, has been previously proposed for the processing of low-grade zinc sulfide concentrates. In this study, we carried out the process of complete biological oxidation of the product of ferric leaching of the zinc concentrate, which contained 9% of sphalerite, 5% of chalcopyrite, and 29.7% of elemental sulfur. After 21 days of biooxidation at 40°C, sphalerite and chalcopyrite oxidation reached 99 and 69%, respectively, while the level of elemental sulfur oxidation was 97%. The biooxidation residue could be considered a waste product that is inert under aerobic conditions. The results of this study showed that zinc sulfide concentrate processing using a two-step treatment is efficient and promising. The microbial community, which developed during biooxidation, was dominated by Acidithiobacillus caldus, Leptospirillum ferriphilum, Ferroplasma acidiphilum, Sulfobacillus thermotolerans, S. thermosulfidooxidans, and Cuniculiplasma sp. At the same time, F. acidiphilum and A. caldus played crucial roles in the oxidation of sulfide minerals and elemental sulfur, respectively. The addition of L. ferriphilum to A. caldus during biooxidation of the ferric leach product proved to inhibit elemental sulfur oxidation.

Challenges and opportunities in the recovery of gold from electronic waste

Rapid global technological development has led to the rising production of electronic waste that presents both challenges and opportunities in its recycling. In this review, we highlight the value of metal resources in the printed circuit boards (PCBs) commonly found in end-of-life electronics, the differences between primary (ore) mining applications and secondary (‘urban’) mining, and the variety of metallurgical separations, in particular those that have the potential to selectively and sustainably recover gold from waste PCBs.

Rapid global technological development has led to the rising production of electronic waste that presents both challenges and opportunities in its recycling.

Consideration of Influential Factors on Bioleaching of Gold Ore Using Iodide-Oxidizing Bacteria

Iodide-oxidizing bacteria (IOB) oxidize iodide into iodine and triiodide which can be utilized for gold dissolution. IOB can be therefore useful for gold leaching. This study examined the impact of incubation conditions such as concentration of the nutrient and iodide, initial bacterial cell number, incubation temperature, and shaking condition on the performance of the gold dissolution through the experiments incubating IOB in the culture medium containing the marine broth, potassium iodide and gold ore. The minimum necessary concentration of marine broth and potassium iodide for the complete gold dissolution were determined to be 18.7 g/L and 10.9 g/L respectively. The initial bacterial cell number had no effect on gold dissolution when it was 1 × 104 cells/mL or higher. Gold leaching with IOB should be operated under a temperature range of 30–35 °C, which was the optimal temperature range for IOB. The bacterial growth rate under shaking conditions was three times faster than that under static conditions. Shaking incubation effectively shortened the contact time compared to the static incubation. According to the pH and redox potential of the culture solution, the stable gold complex in the culture solution of this study could be designated as gold (I) diiodide.

Gold Dissolution from Ore with Iodide-Oxidising Bacteria

Gold leaching from ore using iodide-iodine mixtures is an alternative to gold cyanidation. This study evaluated the ability of iodide-oxidising bacteria to solubilise gold from ore that was mainly composed of gold, pyrite, galena, and chalcopyrite. Eight bacterial strains were successfully isolated from brine. Those strains were incubated in a liquid culture medium containing ore with a gold content of 0.26 wt.% and pulp density of 3.3 w/v% to evaluate their abilities to mediate the dissolution of gold. The gold was solubilised completely within 30 days of incubation in the iodine-iodide lixiviant solution generated by three bacterial strains. One strain, in particular, completed the dissolution of gold within 5 days of incubation and was identified as a member of the genus Roseovarius. Thus, the possibility of bacterial gold leaching using iodide-oxidising bacteria was successfully demonstrated. Bioleaching gold with iodide would likely be more environmentally sustainable than traditional cyanide leaching. Further research is required to evaluate the techno-economic feasibility of this approach.

Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and "A. ferrooxidans" DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and "A. ferrooxidans" DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.

Biotechnology of extremely thermophilic archaea

Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.

Role of microorganisms in bioleaching of rare earth elements from primary and secondary resources

In an era of environmental degradation, and water, and mineral scarcity, enhancing microbial function in sustainable mining has become a prerequisite for the future of the green economy. In recent years, the extensive use of rare earth elements (REEs) in green and smart technologies has led to an increase in the focus on recovery and separation of REEs from ore matrices. However, the recovery of REEs using traditional methods is complex and energy intensive, leading to the requirement to develop processes which are more economically feasible and environmentally friendly. The use of phosphate solubilizing microorganisms for bioleaching of REEs provides a biotechnical approach for the recovery of REEs from primary and secondary sources. However, managing and understanding the microbial-mineral interactions in order to develop a successful method for bioleaching of REEs still remains a major challenge. This review focuses on the use of microbes for the bioleaching of REEs and highlights the importance of genomic studies in order to narrow down potential microorganisms for the optimal extraction of REEs.

Bioleaching of metals from WEEE shredding dust

A bioleaching process developed in two separate steps was investigated for the recovery of base metals, precious metals and rare earth elements from dusts generated by Waste Electrical and Electronic Equipment (WEEE) shredding. In the first step, base metals were almost completely leached from the dust in 8 days by Acidithiobacillus thiooxidans (DSM 9463) that lowered the pH of the leaching solution from 3.5 to 1.0. During this step, cerium, europium and neodymium were mobilized at high percentages (>99%), whereas lanthanum and yttrium reached an extraction yield of 80%. In the second step, the cyanide producing Pseudomonas putida WSC361 mobilized 48% of gold within 3 h from the A. thiooxidans leached shredding dust. This work demonstrated the potential application of biohydrometallurgy for resource recovery from WEEE shredding dust, destined to landfill disposal, and its effectiveness in the extraction of valuable substances, including elements at high supply risk as rare earths.

In a quest for engineering acidophiles for biomining applications: challenges and opportunities

Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.