Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms

Isolation, Sphalerite Bioleaching, and Whole Genome Sequencing of Acidithiobacillus ferriphilus QBS3 from Zinc-Rich Sulfide Mine Drainage

The genus Acidithiobacillus has been widely used in bioleaching, and novel strains in this genus, such as A. ferriphilus, have also been confirmed to possess bioleaching capabilities. In this study, an Acidithiobacillus ferriphilus strain, QBS3, was isolated from zinc-rich sulfide mine drainage using the gradient dilution method. QBS3 is a Gram-negative, 1.3 µm rod-shaped bacterium with small red colonies. It showed a high iron oxidation efficiency of 0.361 g/(L·h) and a sulfur oxidation efficiency of 0.206 g/(L·d). QBS3 has sphalerite bioleaching ability; using QBS3 for pure sphalerite bioleaching, 18.8% of zinc was extracted in 14 days at 1% pulp density. Whole genome sequencing was performed on QBS3. Functional prediction showed that 9.13% of the genes were involved in replication, recombination, and repair. Bioleaching-related genes were analyzed, including iron and sulfur oxidation genes, and carbon and nitrogen fixation genes. For iron oxidation, the Cyc2→RusA pathway and Iro→RusB pathway were found in QBS3. In terms of sulfur oxidation, QBS3 has an incomplete SOX system and lacks the SDO gene, but Rho and Trx may complement the SOX system, enabling QBS3 to oxidize sulfur. QBS3 has multiple sets of carbon fixation genes, and nitrogen fixation genes were also identified. A hypothetical sphalerite bioleaching model is proposed; this study provides a theoretical basis for the zinc sulfide ore bioleaching industry.

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.

Pyrite stimulates the growth and sulfur oxidation capacity of anoxygenic phototrophic sulfur bacteria in euxinic environments

Anoxygenic phototrophic sulfur bacteria flourish in contemporary and ancient euxinic environments, driving the biogeochemical cycles of carbon and sulfur. However, it is unclear how these strict anaerobes meet their high demand for iron in iron-depleted environments. Here, we report that pyrite, a widespread and highly stable iron sulfide mineral in anoxic, low-temperature environments, can support the growth and metabolic activity of anoxygenic phototrophic sulfur bacteria by serving as the sole iron source under iron-depleted conditions. Transcriptomic and proteomic analyses revealed that pyrite addition substantially up-regulated genes and protein expression involved in photosynthesis, sulfur metabolism, and biosynthesis of organics. Anoxic microbial oxidation of pyritic sulfur and consequent destabilization of the pyrite structure were postulated to facilitate microbial iron acquisition. These findings advance our understanding of the survival strategies of anaerobes in iron-depleted environments and are important for revealing the previously underappreciated bioavailability of pyritic iron in anoxic environments and anoxic weathering of pyrite.

Adaptive response of the holdase chaperone network of Acidithiobacillus ferrooxidans ATCC 23270 to stresses and energy sources

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium belonging to microbial communities involved in sulfide ore bioleaching. This microorganism possesses redundancy of genes encoding ATP-independent chaperone holdases like Hsp20 (hps20.1, hsp20.2, and hsp20.3), Hsp31, Hsp33, RidA (ridA.1 and ridA.2), and Lon (lon.1, lon.2, and lon.3), and single copy genes encoding SlyD and CnoX. We evaluated the response of these holdases to short and long-term stresses induced by changes in temperature (30° to 37 °C), pH (1.6 to 1.2 or 2.0), and oxidative status (1 mM H2O2) as well as to different energy sources (iron, sulfur, pyrite, sphalerite or chalcopyrite). Cells adapted under thermal and oxidative stress conditions showed a generalized upregulation of holdase genes, while short-term stress led to more discrete increases in transcript levels, with only hsp20.2 and hsp31 showing higher mRNA levels. hsp31 was also upregulated under acidic stresses, sulfur and sulfides. hsp20 variants showed different mRNA levels under different conditions, and cnoX was induced under oxidative conditions. Cells cultured on chalcopyrite had similar responses to those grown with peroxide. With some exceptions, stresses led to significant increases in intracellular ROS content, and decreases in ATP. These results pave the way to understanding proteostasis systems in extreme acidophilic bacteria.

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.

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.

A novelty strategy for AMD prevention by biogas slurry: Acetate acid inhibition effect on chalcopyrite biooxidation and leachate

With the widespread application of anaerobic digestion technology, biogas slurry become the main source of organic amendments in practice. Comprehensive studies into the inhibitory effects of low molecular weight (LMW) organic acids, essential components in biogas slurry, on the sulfide minerals biooxidation and its bioleaching (AMD) have been lacking. In this study, acetic acid (AA) served as a representative of LMW organic acids in biogas slurry to investigate its impact on the inhibition of chalcopyrite biooxidation by Acidithiobacillus ferrooxidans (A. ferrooxidans). It was shown that AA could slow down the chalcopyrite biooxidation and inhibit the jarosite formation on the mineral surface. Compared with the control group (0 ppm AA), the sulfate increment in the leachate of the 50 ppm, 100 ppm, and 200 ppm AA-treated groups decreased by 36.4%, 66.8%, and 69.0%, respectively. AA treatment (≥50 ppm) could reduce the oxidation of ferrous ions in the leachate by one order of magnitude. At the same time, the bacterial concentration of the leachate in the 50 ppm, 100 ppm, and 200 ppm AA-treated groups decreased by 70%, 93%, and 94%, respectively. These findings provide a scientific basis for new strategies to utilize biogas slurry for mine remediation and contribute to an enhanced comprehension of organic amendments to prevent AMD in situ in mining soil remediation.

Recent Progress in Molecular Oxygen Activation by Iron-Based Materials: Prospects for Nano-Enabled In Situ Remediation of Organic-Contaminated Sites

In situ chemical oxidation (ISCO) is commonly used for the remediation of contaminated sites, and molecular oxygen (O2) after activation by aquifer constituents and artificial remediation agents has displayed potential for efficient and selective removal of soil and groundwater contaminants via ISCO. In particular, Fe-based materials are actively investigated for O2 activation due to their prominent catalytic performance, wide availability, and environmental compatibility. This review provides a timely overview on O2 activation by Fe-based materials (including zero-valent iron-based materials, iron sulfides, iron (oxyhydr)oxides, and Fe-containing clay minerals) for degradation of organic pollutants. The mechanisms of O2 activation are systematically summarized, including the electron transfer pathways, reactive oxygen species formation, and the transformation of the materials during O2 activation, highlighting the effects of the coordination state of Fe atoms on the capability of the materials to activate O2. In addition, the key factors influencing the O2 activation process are analyzed, particularly the effects of organic ligands. This review deepens our understanding of the mechanisms of O2 activation by Fe-based materials and provides further insights into the application of this process for in situ remediation of organic-contaminated sites.

A review of greener approaches for rare earth elements recovery from mineral wastes

The use of rare earth elements (REE) in many various fields, including high-tech products, increases the demand for these materials day by day. The production of REE from primary sources has expanded in response to increasing demand; however, due to its limited, a more sustainable supply is also started to offer for the REE demand by using secondary sources. The most commonly used metallurgical method for REE recovery is hydrometallurgical processes. However, it has some disadvantages, like pyrometallurgical methods. In the review, studies of the environmental impacts of REE production from primary sources and life cycle assessments of products containing REE were investigated. According to the results, it has been seen that those studies in the literature in which hydrometallurgical methods have changed to more environmentally friendly approaches have begun to increase. In this review, mine wastes, which are secondary sources, were defined, conventional methods of recovery of rare earth elements were discussed, greener approaches to the recovery of REE from these sources were comprehensively examined and studies in the literature were evaluated. Furthermore, it was stated that there are limited studies on green approaches and REE recovery from mineral wastes and that this field is developing with an emphasis on the current outlook and future perspectives.

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.

Evaluation of functional characteristics of Acidithiobacillus thiooxidans microencapsulated in gum arabic by spray-drying as biotechnological tool in the mining industry

The mining and metallurgical industry represents one of the leading causes of environmental pollution. In this context, the optimization of mineral waste management and the efficient extraction of metals of interest becomes an imperative priority for a sustainable future. Microorganisms such as Acidithiobacillus thiooxidans have represented a sustainable and economical alternative in recent years due to their capacity for environmental remediation in bioleaching processes because of their sulfur-oxidizing capacity and sulfuric acid generation. However, its use has been limited due to the reluctance of mine operators because of the constant reproduction of the bacterial culture in suitable media and the care that this entails. In this work, the central objective was to evaluate the functional characteristics of A. thiooxidans, microencapsulated and stored at room temperature for three years in vacuum bags, using a spray drying process with gum arabic as a wall vector. Growth kinetics showed a survival of 80 ± 0.52% after this long period of storage. Also, a qualitative fluorescence technique with a 5-cyano-2-3 ditolyl tetrazolium (CTC) marker was used to determine the respiratory activity of the microorganisms as soon as it was resuspended. On the other hand, the consumption of resuspended sulfur was evaluated to corroborate the correct metabolic functioning of the bacteria, with results of up to 50% sulfur reduction in 16 days and sulfate generation of 513.85 ± 0.4387 ppm and 524.15 ± 0.567 ppm for microencapsulated and non-microencapsulated cultures, respectively. These results demonstrate the success after three years of the microencapsulation process and give guidelines for its possible application in the mining-metallurgical industry.

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.