Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans

The outer membrane in Acidithiobacillus ferrooxidans enables high tolerance to rare earth elements

The development of microbial chassis strains with high rare earth element (REE) tolerance is critical for the advancement of new metal biomining and bioprocessing technologies. In this study, we present a mechanistic understanding of how hyperacidophilic bioleaching organism Acidithiobacillus ferrooxidans resists REE-mediated damage at concentrations of REEs as high as 100 mM, while mesophilic Escherichia coli BL21 is significantly inhibited by far lower concentrations of REEs (IC50 between ~5 µM and ~140 µM depending on the element). Using light microscopy to document physiological changes and fluorescent probes to quantify membrane quality, we prove that cell surface interactions explain REE toxicity and demonstrate its reversibility through the addition of chelators. Removal of the A. ferrooxidans outer membrane and cell wall confers REE sensitivity comparable to that of E. coli, corroborating the importance of the outer membrane surface. To conclude, we present a model of differential REE sensitivity in the two strains tested, with implications for industrial metal bioprocessing.IMPORTANCEDemand for rare earth elements (REEs), a technologically critical group of metals, is rapidly increasing (US Geological Survey, 2024. Mineral commodity summaries. Reston, VA). To expand the supply chain without creating environmentally hazardous conditions, there is growing interest in the application of bioprocessing and bioextraction techniques to REE mining and separation. While REE toxicity has been demonstrated in Escherichia coli and other mesophilic neutrophiles, the effect of REEs on organisms currently used in metal bioleaching has been less studied. We present physiological evidence suggesting that REEs damage the outer membrane of E. coli, resulting in growth inhibition that is reversible by chelation. In contrast, Acidithiobacillus ferrooxidans tolerates saturating REE concentrations without apparent inhibition. This study fills gaps in the rapidly expanding body of literature surrounding REE's impact on microbial physiology. Furthermore, A. ferrooxidans resistance to REEs at saturating concentrations (50-100 mM at pH 1.6) is unprecedented in the literature and demonstrates the potential utility of this organism in REE biotechnology.

Magnetic field-assisted bioleaching of cathode materials from spent Li-ion batteries using Acidithiobacillus ferrooxidans

A relatively weak static magnetic field with field strength is externally applied during the growth of using Acidithiobacillus ferrooxidans and subsequent bioleaching of spent Li-ion batteries (LIBs) to recover Li, Ni, Co, and Mn. 5 mT is the optimal field strength which allows 100 % Li to be recovered from a commercial black mass containing Li[Ni0.6Co0.2Mn0.2]O2 after 3 days of leaching. 85 % Ni, 95 % Co, and 100 % Mn are also recovered as dissolved in biogenic H2SO4 after 3 days. Without the external magnetic field, the leaching efficiency is limited to 20-40 % after the same leaching period. It is shown that the magnetic state of the substrate largely influences bioleaching efficiency since the magnetic enhancement is observed only from paramagnetic and ferromagnetic materials through improved cell attachment and not from antiferromagnetic materials. The proposed magnetic field-assisted bioleaching of spent LIBs using A. ferrooxidans can help the recycling of raw materials back into the circular economy for LIBs.

Overexpression of sulfide:quinone reductase (SQR) in Acidithiobacillus ferrooxidans enhances sulfur, pyrite, and pyrrhotite oxidation

Hydrogen sulfide is produced during the dissolution of some sulfidic minerals and during the microbial metabolism of reduced sulfur compounds. The sulfide:quinone reductase (SQR) enzyme is able to oxidize H2S, and the bioleaching cells Acidithiobacillus ferrooxidans have two SQR genes, only one of which has been characterized. We cloned and overexpressed the two SQR genes in A. ferrooxidans and show that they both have SQR activity. Both AFE_0267 and AFE_1792 are active under anaerobic conditions, but only AFE_1792 is active under aerobic conditions. The effect of the SQR overexpression and the expression of related genes on sulfur metabolism was investigated. The overexpression of SQR improved cell growth and sulfur oxidation, suggesting enhanced SQR activity led to a reduction in H2S toxicity as well as providing additional energy through H2S oxidation. Additionally, the impact on the oxidation of pyrite and pyrrhotite was investigated. The rate of oxidation of pyrite by the engineered cells was enhanced, and, furthermore, the rate of pyrrhotite oxidation was more than doubled.IMPORTANCEH2S is a toxic sulfur intermediate, and the SQR enzyme has evolved to oxidize H2S in A. ferrooxidans. In addition to detoxification, H2S oxidation provides energy, and overexpression of SQR enhanced aerobic and anaerobic growth on sulfur. The SQR overexpression also enhanced pyrite and pyrrhotite oxidation, which may facilitate the pyrometallurgical processing of a number of critical materials including copper, nickel, and the platinum group metals.

Molecular disruptions in microalgae caused by Acidithiobacillus ferrooxidans: Photosynthesis, oxidative stress, and energy metabolism in acid mine drainage

Microalgae are recognized for their potential in the bioremediation of acid mine drainage (AMD), despite the challenges posed by AMD's low pH, high heavy metal content, and oligotrophic conditions. However, the impact of AMD chemoautotrophic microorganisms on microalgal growth and remediation efforts within AMD has been largely overlooked. This study aims to elucidate the effects the chemoautotrophic microorganism, Acidithiobacillus ferrooxidans, on the growth activity and metabolism of acid-tolerant microalgae, and to explore the molecular mechanisms of microalgal response. Our findings reveal that the presence of A. ferrooxidans inhibits the growth and alkaline production of Parachlorella sp. MP1, resulting in a 90.86 % reduction in biomass. Physiological, biochemical, and transcriptomic studies, indicate that oxidative stress, photosynthesis, and energy metabolism are the metabolic processes most affected by A. ferrooxidans. Specifically, A. ferrooxidans introduces an increased production of reactive oxygen species (ROS) in Parachlorella sp. MP1, leading to an upregulation of genes and enzymes associated with peroxisome activity and intensifying oxidative stress within the cells. Downregulation of photosynthesis-related genes disrupts the electron transport chain, inhibiting photosynthesis. Furthermore, alterations in the gene expression of pyruvate and acetyl-CoA metabolic pathways result in energetic pathway disruption. These insights contribute to a better understanding of how A. ferrooxidans influence the growth metabolism of acid-tolerant microalgae in AMD environments and inform the optimization of microalgal application strategies in AMD bioremediation engineering.

Site Directed Mutagenesis of the Cyc2 Outer Membrane Protein from Acidithiobacillus ferrooxidans Reveals a Critical Role for Bound Iron Atoms in Extracellular Electron Transfer

Extracellular electron transfer (EET) processes by metal respiratory bacteria rely on outer membrane proteins (OMPs) to exchange electrons across the insulating cell membrane. The most studied OMPs from metal reducing bacteria contain multiple sequential heme groups. However, many iron-oxidizing bacteria, including the industrial bioleaching microbe Acidithiobacillus ferrooxidans, contain monoheme OMPs and the mechanism of electron transfer through these smaller structures has not been elucidated. Computational modeling was previously used to predict two iron ion binding sites in the Cyc2 protein structure from A. ferrooxidans. To determine if these binding sites are critical for protein function, the monoheme Cyc2 OMP from A. ferrooxidans is recombinantly expressed in E. coli outer membrane vesicles (OMVs) which are then incorporated into biomimetic cell-membrane supported lipid bilayers (SLB) on electrodes to measure electron transfer. Site-directed mutagenesis is used to disrupt the putative ion binding sites predicted from modeling to elucidate the mechanism. It is confirmed that the Cyc2 protein is capable of EET without the need for soluble iron or other accessory proteins. These results confirm the critical role of bound metal ions in the A. ferrooxidans EET mechanism, and it is expected that homologous monoheme OMPs will have similar conduction pathways.

Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota

It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth, with metabolically versatile members colonizing a wide range of environments with different O2 concentrations. Here, we address this question by studying isoprenoid quinones, which are central components of energy metabolism covering a wide range of redox potentials. We demonstrate that a dynamic repertoire of quinone biosynthetic pathways accompanied the diversification of Pseudomonadota. The low potential menaquinone (MK) was lost in an ancestor of Pseudomonadota while the high potential ubiquinone (UQ) emerged. We show that the O2-dependent and O2-independent UQ pathways were both present in the last common ancestor of Pseudomonadota, and transmitted vertically. The O2-independent pathway has a conserved genetic organization and displays signs of positive regulation by the master regulator "fumarate and nitrate reductase" (FNR), suggesting a conserved role for UQ in anaerobiosis across Pseudomonadota. The O2-independent pathway was lost in some lineages but maintained in others, where it favoured a secondary reacquisition of low potential quinones (MK or rhodoquinone), which promoted diversification towards aerobic facultative and anaerobic metabolisms. Our results support that the ecological success of Pseudomonadota is linked to the acquisition of the largest known repertoire of quinones, which allowed adaptation to oxic niches as O2 levels increased on Earth, and subsequent diversification into anoxic or O2-fluctuating environments.

Multi-stress adaptive lifestyle of acidophiles enhances their robustness for biotechnological and environmental applications

Acidophiles are a group of organisms typically found in highly acidic environments such as acid mine drainage. These organisms have several physiological features that enable them to thrive in highly acidic environments (pH ≤3). Considering that both acid mine drainage and solfatara fields exhibit extreme and dynamic ecological conditions for acidophiles, it is crucial to gain deeper insights into the adaptive mechanisms employed by these unique organisms. The existing literature reveals a notable gap in understanding the multi-stress conditions confronting acidophiles and their corresponding coping mechanisms. Therefore, the current review aims to illuminate the intricacies of the metabolic lifestyles of acidophiles within these demanding habitats, exploring how their energy demands contribute to habitat acidification. In addition, the unique adaptive mechanisms employed by acidophiles were emphasized, especially the pivotal role of monolayer membrane-spanning lipids, and how these organisms effectively respond to a myriad of stresses. Beyond mere survival, understanding the adaptive mechanisms of these unique organisms could further enhance their use in some biotechnological and environmental applications. Lastly, this review explores the strategies used to engineer these organisms to promote their use in industrial applications.

The effect of calcium on the removal of Cd2+ in the formation of biogenic secondary iron minerals

Cadmium is a toxic heavy metal found in acid mine drainage. It hinders plant and animal growth and accumulates in human organs. In this study, through shake flask experiments, an iron-rich, sulphate-rich environment was simulated, and Acidithiobacillus ferrooxidans was used to mediate the formation of secondary high-iron minerals to explore the effect of calcium ions on the removal of Cd2+ from that environment. Four treatment systems were used: "Blank", "Ca2+-30 mg/L", "Fe/K = 3,Ca2+-30 mg/L", and "Fe/K = 3". The results showed that Cd2+ with an initial concentration of 20 mg/L was effectively removed in each treatment system. The removal efficiencies of Cd2+ in each treatment were 23.46%, 18.42%, 52.88%, and 45.76% respectively. The quantity and type of minerals determined the removal efficiency of Cd2+. The Fe/K = 3 treatment system can significantly increase the amount of mineral formation and improve the removal efficiency of Cd2+. In the Ca2+-30 mg/L, Fe/K = 3 treatment system, the biological oxidation ability was the strongest, and the removal effect of Cd2+ was the best under the combined action of K+ and Ca2+. Co-precipitation was the main way to remove Cd2+ during the formation of biogenic secondary iron minerals, and the removal amount was 5.64 to 14.83 times that of adsorption. Biogenetic secondary iron minerals showed high values in repairing heavy metal pollution. This study provides a theoretical basis for treating heavy metals in acid mine drainage.

Enhanced bioleaching of spent Li-ion batteries using A. ferrooxidans by application of external magnetic field

Recycling spent batteries is increasingly important for the sustainable use of Li-ion batteries (LIBs) and for countering the supply uncertainty of critical raw minerals (Li, Co, and Ni). Bioleaching, which uses microorganisms to extract valuable metals, is both economical and environmentally safe compared to other recycling methods, but its practical application is impaired by slow kinetics. Accelerating the process is a key for bioleaching spent LIBs on an industrial scale. Acidithiobacillus ferrooxidans (A. ferrooxidans), which thrives in extremely low pH conditions, has long been explored for bioleaching of spent LIBs. Metabolism of A. ferrooxidans involves the oxidation of magnetic Fe2+ and produces intracellular magnetic nanoparticles. The possibility of accelerating the leaching kinetics of A. ferrooxidans by the application of an external magnetic field is explored in this work. A weak static magnetic field is applied during the bioleaching of spent LIBs to recover Li, Ni, and Co using A. ferrooxidans. It is determined that 3 mT is the optimal field strength which allows the leaching efficiency of Li to reach 100% after only 2 days of leaching at a pulp density of 3 w/v % while without the external magnetic field, the leaching efficiency is limited to 57% even after 4 days. The leaching efficiency of Ni and Co also increases by nearly three-fold to >80% after 4 days of leaching. The proposed magnetic field-assisted bioleaching of spent LIBs using A. ferrooxidans substantially improves the leaching kinetics and thus the cost-effectiveness of the bioleaching process with minimal environmental impact, hence enabling environment-friendly recycling of raw materials that are increasingly becoming scarce. The positive effect of an external magnetic field on the metabolism of A. ferrooxidans demonstrated in this work provide a new set of tools to engineer the bioleaching process and the possibility for genetic modification of acidophile bacteria, especially targeted for magnetic enhancement.

CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc1 complexes enables enhanced metal sulfide bioleaching

Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important role in biogeochemical iron and sulfur cycling and is a member of the consortia used in industrial hydrometallurgical processing of copper. Metal sulfide bioleaching is catalyzed by the regeneration of ferric iron; however, bioleaching of chalcopyrite, the dominant unmined form of copper on Earth, is inhibited by surface passivation. Here, we report the implementation of CRISPR interference (CRISPRi) using the catalytically inactive Cas12a (dCas12a) in A. ferrooxidans to knock down the expression of genes in the petI and petII operons. These operons encode bc1 complex proteins and knockdown of these genes enabled the manipulation (enhancement or repression) of iron oxidation. The petB2 gene knockdown strain enhanced iron oxidation, leading to enhanced pyrite and chalcopyrite oxidation, which correlated with reduced biofilm formation and decreased surface passivation of the minerals. These findings highlight the utility of CRISPRi/dCas12a technology for engineering A. ferrooxidans while unveiling a new strategy to manipulate and improve bioleaching efficiency.

Overexpression of a Designed Mutant Oxyanion Binding Protein ModA/WtpA in Acidithiobacillus ferrooxidans for the Low pH Recovery of Molybdenum and Rhenium

Molybdenum and rhenium are critically important metals for a number of emerging technologies. We identified and characterized a molybdenum/tungsten transport protein (ModA/WtpA) of Acidithiobacillus ferrooxidans and demonstrated the binding of tungstate, molybdate, and chromate. We used computational design to expand the binding capabilities of the protein to include perrhenate. A disulfide bond was engineered into the binding pocket of ModA/WtpA to introduce a more favorable geometric coordination and surface charge distribution for oxyanion binding. The mutant protein experimentally demonstrated a 2-fold higher binding affinity for molybdate and 6-fold higher affinity for perrhenate. The overexpression of the wild-type and mutant ModA/WtpA proteins in A. ferrooxidans cells enhanced the innate tungstate, molybdate, and chromate binding capacities of the cells to up to 2-fold higher. In addition, the engineered cells expressing the mutant protein exhibited enhanced perrhenate binding, showing 5-fold and 2-fold higher binding capacities compared to the wild-type and ModA/WtpA-overexpressing cells, respectively. Furthermore, the engineered cell lines enhanced biocorrosion of stainless steel as well as the recovered valuable metals from an acidic wastewater generated from molybdenite processing. The improved binding efficiency for the oxyanion metals, along with the high selectivity over nontargeted metals under mixed metal environments, highlights the potential value of the engineered strains for practical microbial metal reclamation under low pH conditions.

Research on the decomposition mechanisms of lithium silicate ores with different crystal structures by autotrophic and heterotrophic bacteria

Ores serve as energy and nutrient sources for microorganisms. Through complex biochemical processes, microorganisms disrupt the surface structure of ores and release metal elements. However, there is limited research on the mechanisms by which bacteria with different nutritional modes act during the leaching process of different crystal structure ores. This study evaluated the leaching efficiency of two types of bacteria with different nutritional modes, heterotrophic bacterium Bacillus mucilaginosus (BM) and autotrophic bacterium Acidithiobacillus ferrooxidans (AF), on different crystal structure lithium silicate ores (chain spodumene, layered lepidolite and ring elbaite). The aim was to understand the behavioral differences and decomposition mechanisms of bacteria with different nutritional modes in the process of breaking down distorted crystal lattices of ores. The results revealed that heterotrophic bacterium BM primarily relied on passive processes such as bacterial adsorption, organic acid corrosion, and the complexation of small organic acids and large molecular polymers with metal ions. Autotrophic bacterium AF, in addition to exhibiting stronger passive processes such as organic acid corrosion and complexation, also utilized an active transfer process on the cell surface to oxidize Fe2+ in the ores for energy maintenance and intensified the destruction of ore lattices. As a result, strain AF exhibited a greater leaching effect on the ores compared to strain BM. Regarding the three crystal structure ores, their different stacking modes and proportions of elements led to significant differences in structural stability, with the leaching effect being highest for layered structure, followed by chain structure, and then ring structure. These findings indicate that bacteria with different nutritional modes exhibit distinct physiological behaviors related to their nutritional and energy requirements, ultimately resulting in different sequences and mechanisms of metal ion release from ores after lattice damage.

Characterize the Growth and Metabolism of Acidithiobacillus ferrooxidans under Electroautotrophic and Chemoautotrophic Conditions

Acidophiles are capable of surviving in extreme environments with low pH. Acidithiobacillus ferrooxidans is a typical acidophilic bacterium that has been extensively studied when grown chemoautotrophically, i.e., when it derives energy from oxidation of Fe2+ or reduced inorganic sulfur compounds (RISCs). Although it is also known to grow with electrons supplied by solid electrodes serving as the sole source of energy, the understanding of its electroautotrophic growth is still limited. This study aimed to compare the growth characteristics of A. ferrooxidans under electroautotrophic (ea) and chemoautotrophic (ca) conditions, with an attempt to elucidate the possible mechanism(s) of extracellular electron flow into the cells. Jarosite was identified by Raman spectroscopy, and it accumulated when A. ferrooxidans used Fe2+ as the electron donor, but negligible mineral deposition occurred during electroautotrophic growth. Scanning electron microscopy (SEM) showed that A. ferrooxidans possesses more pili and extracellular polymeric substances (EPSs) under electroautotrophic conditions. A total of 493 differentially expressed genes (DEGs) were identified, with 297 genes being down-regulated and 196 genes being up-regulated in ea versus ca conditions. The genes known to be essential for chemoautotrophic growth showed a decreased expression in the electroautotrophic condition; meanwhile, there was an increased expression of genes related to direct electron transfer across the cell's outer/inner membranes and transmembrane proteins such as pilin and porin. Joint analysis of DEGs and differentially expressed metabolites (DEMs) showed that galactose metabolism is enhanced during electroautotrophic growth, inducing A. ferrooxidans to produce more EPSs, which aids the cells in adhering to the solid electrode during their growth. These results suggested that electroautotrophy and chemoautotrophy of A. ferrooxidans have different extracellular electron uptake (EEU) pathways, and a model of EEU during electroautotrophic growth is proposed. The use of extracellular electrons as the sole energy source triggers A. ferrooxidans to adopt metabolic and subsequently phenotypic modifications.

Significant differences in the degree of genomic DNA N6-methyladenine modifications in Acidithiobacillus ferrooxidans with two different culture substrates

DNA N6-methyladenine (6mA) modification is widespread in organisms and plays an important functional role in the regulation of cellular processes. As a model organism in biohydrometallurgy, Acidithiobacillus ferrooxidans can obtain energy from the oxidation of ferrous iron (Fe2+) and various reduced inorganic sulfides (RISCs) under acidic conditions. To determine the linkage between genomic DNA methylation and the switching between the two oxidative metabolic pathways in A. ferrooxidans, the 6mA landscape in the genome of A. ferrooxidans cultured under different conditions was evaluated by using 6mA-IP-seq. A total of 214 and 47 high-confidence peaks of 6mA were identified under the Fe2+ and RISCs oxidizing conditions, respectively (P<10-5), suggesting that genomic methylation was greater under Fe2+ oxidizing conditions. 6mA experienced a decline at the transcription start site (TSS) and occurs frequently in gene bodies under both oxidizing conditions. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that 7 KEGG pathways were mapped into and most of the differentially methylated genes were enriched in oxidative phosphorylation and metabolic pathways. Fourteen genes were selected for studying the effect of differences in methylation on mRNA expression. Thirteen genes, excluding petA-1, demonstrated a decrease in mRNA expression as methylation levels increased. Overall, the 6mA methylation enrichment patterns are similar under two conditions but show differences in the enriched pathways. The phenomenon of upregulated gene methylation levels coupled with downregulated expression suggests a potential association between the regulation mechanisms of 6mA and the Fe2+ and RISCs oxidation pathways.

Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe3O4 nanoparticles in Acidithiobacillus ferrooxidans BYM

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.

Genetic Modification of Acidithiobacillus ferrooxidans for Rare-Earth Element Recovery under Acidic Conditions

As global demands for rare-earth elements (REEs) continue to grow, the biological recovery of REEs has been explored as a promising strategy, driven by potential economic and environmental benefits. It is known that calcium-binding domains, including helix-loop-helix EF hands and repeats-in-toxin (RTX) domains, can bind lanthanide ions due to their similar ionic radii and coordination preference to calcium. Recently, the lanmodulin protein from Methylorubrum extorquens was reported, which has evolved a high affinity for lanthanide ions over calcium. Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile, which has been explored for use in bioleaching for metal recovery. In this report, A. ferrooxidans was engineered for the recombinant intracellular expression of lanmodulin. In addition, an RTX domain from the adenylate cyclase protein of Bordetella pertussis, which has previously been shown to bind Tb3+, was expressed periplasmically via fusion with the endogenous rusticyanin protein. The binding of lanthanides (Tb3+, Pr3+, Nd3+, and La3+) was improved by up to 4-fold for cells expressing lanmodulin and 13-fold for cells expressing the RTX domains in both pure and mixed metal solutions. Interestingly, the presence of lanthanides in the growth media enhanced protein expression, likely by influencing protein stability. Both engineered cell lines exhibited higher recoveries and selectivities for four tested lanthanides (Tb3+, Pr3+, Nd3+, and La3+) over non-REEs (Fe2+ and Co2+) in a synthetic magnet leachate, demonstrating the potential of these new strains for future REE reclamation and recycling applications.

From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus

Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.

Molecular Identification and Acid Stress Response of an Acidithiobacillus thiooxidans Strain Isolated from Rio Tinto (Spain)

Acidithiobacillus thiooxidans is of paramount importance in the development of biomining technologies. Being widely recognized as an extreme acidophile, extensive research has been dedicated to understanding its significant role in the extraction of several ores in recent years. However, there still exist significant molecular uncertainties surrounding this species. This study focuses on developing a taxonomic assignment method based on the sequencing of the 16S-5S rRNA cluster, along with a qPCR-based technology enabling precise growth determination. Additionally, an approach to understanding its response to acid stress is explored through RT-PCR and MALDI-TOF analysis. Our findings indicate that when subjected to pH levels below 1, the cell inhibits central (carbon fixation and metabolism) and energy (sulfur metabolism) metabolism, as well as chaperone synthesis, suggesting a potential cellular collapse. Nevertheless, the secretion of ammonia is enhanced to raise the environmental pH, while fatty acid synthesis is upregulated to reinforce the cell membrane.

Overexpression of quorum sensing genes in Acidithiobacillus ferrooxidans enhances cell attachment and covellite bioleaching

Cell adhesion is generally a prerequisite to the microbial bioleaching of sulfide minerals, and surface biofilm formation is modulated via quorum sensing (QS) communication. We explored the impact of the overexpression of endogenous QS machinery on the covellite bioleaching capabilities of Acidithiobacillus ferrooxidans, a representative acidophilic chemolithoautotrophic bacterium. Cells were engineered to overexpress the endogenous qs-I operon or just the afeI gene under control of the tac promoter. Both strains exhibited increased transcriptional gene expression of afeI and improved cell adhesion to covellite, including increased production of extracellular polymeric substances and increased biofilm formation. Under low iron conditions, the improved bioleaching of covellite was more evident when afeI was overexpressed alone as compared to the native operon. These observations demonstrate the potential for the genetic modulation of QS as a mechanism for increasing the bioleaching efficiency of covellite, and potentially other copper sulfide minerals.

Recent progress in the synthesis of advanced biofuel and bioproducts

Energy is one of the most complex fields of study and an issue that influences nearly every aspect of modern life. Over the past century, combustion of fossil fuels, particularly in the transportation sector, has been the dominant form of energy release. Refining of petroleum and natural gas into liquid transportation fuels is also the centerpiece of the modern chemical industry used to produce materials, solvents, and other consumer goods. In the face of global climate change, the world is searching for alternative, sustainable means of producing energy carriers and chemical building blocks. The use of biofuels in engines predates modern refinery optimization and today represents a small but significant fraction of liquid transportation fuels burnt each year. Similarly, white biotechnology has been used to produce many natural products through fermentation. The evolution of recombinant DNA technology into modern synthetic biology has expanded the scope of biofuels and bioproducts that can be made by biocatalysts. This opinion examines the current trends in this research space, highlighting the substantial growth in computational tools and the growing influence of renewable electricity in the design of metabolic engineering strategies. In short, advanced biofuel and bioproduct synthesis remains a vibrant and critically important field of study whose focus is shifting away from the conversion of lignocellulosic biomass toward a broader consideration of how to reduce carbon dioxide to fuels and chemical products.

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.

Advances in bioleaching of waste lithium batteries under metal ion stress

In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.

Effects of Initial pH and Carbonate Rock Dosage on Bio-Oxidation and Secondary Iron Mineral Synthesis

The effect of pH is a key factor in biomineralization mediated by Acidithiobacillus ferrooxidans to promote the transformation of Fe into secondary iron minerals. This study aimed to investigate the effects of initial pH and carbonate rock dosage on bio-oxidation and secondary iron mineral synthesis. Variations in pH and the concentrations of Ca²⁺, Fe²⁺, and total Fe (TFe) in the growth medium of A. ferrooxidans were examined in the laboratory to determine how they affect the bio-oxidation process and secondary iron mineral synthesis. The results showed that in systems with an initial pH of 1.8, 2.3, and 2.8, the optimum dosages of carbonate rock were 30, 10, and 10 g, respectively, which significantly improved the removal rate of TFe and the amount of sediments. At an initial pH of 1.8 and a carbonate rock dosage of 30 g, the final removal rate of TFe reached 67.37%, which was 28.03% higher than that of the system without the addition of carbonate rock, and 36.9 g·L^-1 of sediments were generated, which was higher than that of the system without the addition of carbonate rock (6.6 g·L^-1). Meanwhile, the number of sediments generated by adding carbonate rock were significantly higher than those without the addition of carbonate rock. The secondary minerals were characterized by a progressive transition from low crystalline assemblages composed of calcium sulfate and subordinated jarosite, to well crystal-line assemblages composed of jarosite, calcium sulfate, and goethite. These results have important implications for comprehensively understanding the dosage of carbonate rock in mineral formation under different pH conditions. The findings help reveal the growth of secondary minerals during the treatment of AMD using carbonate rocks under low-pH conditions, which offers valuable information for combining the carbonate rocks with secondary minerals to treat AMD.

Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives

With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.

Harnessing synthetic biology for sustainable biomining with Fe/S-oxidizing microbes

Biomining is a biotechnological approach where microorganisms are used to recover metals from ores and waste materials. While biomining applications are motivated by critical issues related to the climate crisis (e.g., habitat destruction due to mine effluent pollution, metal supply chains, increasing demands for cleantech-critical metals), its drawbacks hinder its widespread commercial applications: lengthy processing times, low recovery, and metal selectivity. Advances in synthetic biology provide an opportunity to engineer iron/sulfur-oxidizing microbes to address these limitations. In this forum, we review recent progress in synthetic biology-enhanced biomining with iron/sulfur-oxidizing microbes and delineate future research avenues.

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle

Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.