Addition of citrate to Acidithiobacillus ferrooxidans cultures enables precipitate-free growth at elevated pH and reduces ferric inhibition

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.

Investigating the acidophilic microbial community's adaptation for enhancement indium bioleaching from high pulp density shredded discarded LCD panels

As part of electronic waste (e-waste), the fastest growing solid waste stream in the world, discarded liquid crystal displays (LCDs) contain substantial amounts of both valuable and potentially harmful metal, offering valuable opportunities for resource extraction but posing environmental threats. The present comprehensive study is an investigation into the bioleaching of indium from discarded LCD panels, with a particular focus on high pulp density shredded (Sh-LCDs) and powdered (P-LCDs) materials. This study involved an acidophilic consortium, with two pathways, namely the mixed sulfur-iron pathways and sulfur pathways, being explored to understand the bioleaching mechanisms. Indium bioleaching efficiencies through the mixed sulfur-iron pathway were approximately 60% and 100% for Sh-LCDs and P-LCDs, respectively. Three mechanisms were involved in the extraction of indium from LCD samples: acidolysis, complexolysis, and redoxolysis. The microbial community adapted to a pulp density of 32.5 g/L was streak-plated and it was revealed that sulfur-oxizing bacteria dominated, resulting in the minimum indium extraction of 10% and 55% for both Sh-LCDs and P-LCDs samples, respectively. It was generally accepted that ferric ions as oxidants were effective for indium bioleaching from both the Sh-LCDs and P-LCDs. This implies that the cooperation or interaction within the microbial community used in the bioleaching process had a beneficial impact, enhancing the overall effectiveness of extracting indium from LCD panels. The adapted consortium utilizes a combination of microbial transformation, efflux systems, and chelation through extracellular substances to detoxify heavy metals. The adapted microbial community demonstrated better indium leaching efficiency (50%) compared to the non-adapted microbial community which achieved a maximum of 29% and 5% respectively from Sh-LCDs and P-LCDs at a pulp density of 32.5 g/L. The advantages of an adapted microbial community for indium leaching efficiency, attributing this advantage to factors such as high metabolic activity and improved tolerance to heavy metals. Additionally, the protective role of the biofilm formed by the adapted microbial community is particularly noteworthy, as it contributes to the community's resilience in the presence of inhibitory substances. This information is valuable for understanding and optimizing bioleaching processes for indium recovery, and by extension to possibly other metals.

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.

Magnetosome yield characteristics modeling of acidithiobacillus ferrooxidans in airlift bioreactor using response surface methodology

Bacterial magnetosomes had been proved to have great application potential in medicine and biotechnology. The objective of the present study was to obtain high yield of magnetosomes from Acidithiobacillus ferrooxidans (A. ferrooxidans) BYM in an airlift bioreactor using response surface methodology (RSM). The magnetosomes from A. ferrooxidans BYM were characterized using a transmission electron microscope and scanning electron microscopy. The maximum magnetosome yield of 0.4267 mg/L was achieved at ventilation capacity of 3.6 L/min and gluconic acid concentration of 10 mmol/L at 25^oC. The correlation coefficient (R²) value of 0.8676 of the obtained model suggested a good correlation between the actual and predicted magnetosome yield. The confirmation experiment confirmed that the actual magnetosome yield of 0.391 mg/L obtained were in agreement with the predicted value of 0.398 mg/L. These results suggested that RSM can be employed to find out the optimum conditions for magnetosome formation in airlift bioreactor.

Engineering Polyhistidine Tags on Surface Proteins of Acidithiobacillus ferrooxidans: Impact of Localization on the Binding and Recovery of Divalent Metal Cations

Metal processing using microorganisms has many advantages including the potential for reduced environmental impacts as compared to conventional technologies.Acidithiobacillus ferrooxidansis an iron- and sulfur-oxidizing chemolithoautotroph that is known to participate in metal bioleaching, and its metabolic capabilities have been exploited for industrial-scale copper and gold biomining. In addition to bioleaching, microorganisms could also be engineered for selective metal binding, enabling new opportunities for metal bioseparation and recovery. Here, we explored the ability of polyhistidine (polyHis) tags appended to two recombinantly expressed endogenous proteins to enhance the metal binding capacity of A. ferrooxidans. The genetically engineered cells achieved enhanced cobalt and copper binding capacities, and the Langmuir isotherm captures their interaction behavior with these divalent metals. Additionally, the cellular localization of the recombinant proteins correlated with kinetic modeling of the binding interactions, where the outer membrane-associated polyHis-tagged licanantase peptide bound the metals faster than the periplasmically expressed polyHis-tagged rusticyanin protein. The selectivity of the polyHis sequences for cobalt over copper from mixed metal solutions suggests potential utility in practical applications, and further engineering could be used to create metal-selective bioleaching microorganisms.

Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans

There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.

Selective removal of cobalt and copper from Fe (III)-enriched high-pressure acid leach residue using the hybrid bioleaching technique

Removal of metals from high pressure acid leaching (HPAL) residue was essential to alleviate potential environmental threat and avoid valuable metals loss. However, cost-effective metals extraction from HPAL residue remains a difficulty. In this study, a hybrid bioleaching process was developed for Co and Cu extraction from HPAL residue of Cu-Co sulfide ores. Results for microbial community structure optimization showed that moderate thermophilum consortium with coexistence of iron oxidizer and sulfur oxidizer was more efficient on metal extraction compared with mesophiles. Further addition of citric acid, Fe (II) and S⁰ significantly enhanced the release of metals through improving the total biomass, attached cells and community diversity. As a result, 87.91% of cobalt and 58.52% of copper were extracted at initial pH 1.4 and pulp density of 50 g/L by hybrid bioleaching. The hazardous potential assessments revealed that the bioleached residue could be disposed safely. These findings demonstrated that organic acids assisting bioleaching with community adjusting was a promising strategy for metals removal from HPAL residue.

Microbially Influenced Corrosion of Stainless Steel by Acidithiobacillus ferrooxidans Supplemented with Pyrite: Importance of Thiosulfate

Microbially influenced corrosion (MIC) results in significant damage to metallic materials in many industries. Anaerobic sulfate-reducing bacteria (SRB) have been well studied for their involvement in these processes. Highly corrosive environments are also found in pulp and paper processing, where chloride and thiosulfate lead to the corrosion of stainless steels. Acidithiobacillus ferrooxidans is a critically important chemolithotrophic acidophile exploited in metal biomining operations, and there is interest in using A. ferrooxidans cells for emerging processes such as electronic waste recycling. We explored conditions under which A. ferrooxidans could enable the corrosion of stainless steel. Acidic medium with iron, chloride, low sulfate, and pyrite supplementation created an environment where unstable thiosulfate was continuously generated. When combined with the chloride, acid, and iron, the thiosulfate enabled substantial corrosion of stainless steel (SS304) coupons (mass loss, 5.4 ± 1.1 mg/cm² over 13 days), which is an order of magnitude higher than what has been reported for SRB. There results were verified in an abiotic flow reactor, and the importance of mixing was also demonstrated. Overall, these results indicate that A. ferrooxidans and related pyrite-oxidizing bacteria could produce aggressive MIC conditions in certain environmental milieus.IMPORTANCE MIC of industrial equipment, gas pipelines, and military material leads to billions of dollars in damage annually. Thus, there is a clear need to better understand MIC processes and chemistries as efforts are made to ameliorate these effects. Additionally, A. ferrooxidans is a valuable acidophile with high metal tolerance which can continuously generate ferric iron, making it critical to copper and other biomining operations as well as a potential biocatalyst for electronic waste recycling. New MIC mechanisms may expand the utility of these cells in future metal resource recovery operations.

Bioleaching of heavy metals from harbor sediment using sulfur-oxidizing microflora acclimated from native sediment and exogenous soil

The harbor sediment containing high concentration of heavy metals may pose serious impacts on the marine ecosystem and environmental quality. The bioleaching process has been considered as an environmentally friendly and cost-effective alternative for removing heavy metals from contaminated sediments. In this study, a series of experiments were performed to investigate the feasibility of bioleaching process for removing heavy metals from the contaminated harbor sediments. The performance of the bioleaching process inoculated with sulfur-oxidizing microflora acclimated from the native harbor sediment was compared with that acclimated from the exogenous soil. In the bioleaching experiment with inoculants from native sediment, the efficiency of Zn, Cu, Cr, Pb, and Ni (30 days) reached 39-100%, 21-94%, 8-63%, 5-74%, and 19-77%, respectively. While 59-100% of Zn, 22-100% of Cu, 0-95% of Cr, 0-100% of Pb, and 22-100% of Ni were respectively removed in the bioleaching experiment with inoculants from exogenous soil after 30 days of reaction time. The results show that the rate and efficiency of metal removal in the bioleaching process decreased with an increase of sediment solid content from 10 to 40 g/L. The efficiency of metal removal in the bioleaching process with inoculants from the native sediment was lower than those from the exogenous soil due to the bacterial activity. By the fractionation of metal in the harbor sediment, exchangeable, carbonate-bound, and Fe/Mn oxide-bound metals (mobile fractions) were found to be apparently reduced and even organic matter/sulfide-bound and residual metals (stable fractions) were slightly removed after the bioleaching experiment.

Transposase-Mediated Chromosomal Integration of Exogenous Genes in Acidithiobacillus ferrooxidans

The development of Acidithiobacillus ferrooxidans as a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used to identify the insertion sites of the KDC gene in several mutants, leading to the identification of a region on the chromosome that may be suitable for future genetic insertions. These results demonstrate that functional exogenous metabolic genes have been chromosomally integrated into A. ferrooxidans, and this advance will facilitate the future development of these cells for new biotechnology applications.IMPORTANCE Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph and is a key member of the microbial consortia used in industrial biomining applications. There is interest in exploiting these cells for other metal recovery applications as well as in developing them as unique nonmodel microbial cell factories. Plasmid-driven expression of exogenous genes has been reported, and homologous recombination has been used to knock out some gene expression. Here, new selection protocols facilitated the development of a transposition method for chromosomal integration of exogenous genes into A. ferrooxidans This greatly expands the available genetic toolbox, which will open the door to greater metabolic engineering efforts for these cells.

Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals

The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms.