Identification and Analysis of a Novel Gene Cluster Involves in Fe2+ Oxidation in Acidithiobacillus ferrooxidans ATCC 23270, a Typical Biomining Acidophile

Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation

IMPORTANCE

Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.

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.

Ferric Iron Reduction in Extreme Acidophiles

Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.

Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments

Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.

Bioinformatics and Transcriptional Study of the Nramp Gene in the Extreme Acidophile Acidithiobacillus ferrooxidans Strain DC

The family of Nramp (natural resistance-associated macrophage protein) metal ion transporter functions in diverse organisms from bacteria to humans. Acidithiobacillus ferrooxidans (At. ferrooxidans) is a Gram-negative bacterium that lives at pH 2 in high concentrations of soluble ferrous ion (600 mM). The AFE_2126 protein of At. ferrooxidans of the Dachang Copper Mine (DC) was analyzed by bioinformatics software or online tools, showing that it was highly homologous to the Nramp family, and its subcellular localization was predicted to locate in the cytoplasmic membrane. Transcriptional study revealed that AFE_2126 was expressed by Fe2+-limiting conditions in At. ferrooxidans DC. It can be concluded that the AFE_2126 protein may function in ferrous ion transport into the cells. Based on the ΔpH of the cytoplasmic membrane between the periplasm (pH 3.5) and the cytoplasm (pH 6.5), it can be concluded that Fe2+ is transported in the direction identical to that of the H+ gradient. This study indirectly confirmed that the function of Nramp in At. ferrooxidans DC can transport divalent iron ions.

Effective Treatment of Acid Mine Drainage with Microbial Fuel Cells: An Emphasis on Typical Energy Substrates

Acid mine drainage (AMD), characterized by a high concentration of heavy metals, poses a threat to the ecosystem and human health. Bioelectrochemical system (BES) is a promising technology for the simultaneous treatment of organic wastewater and recovery of metal ions from AMD. Different kinds of organic wastewater usually contain different predominant organic chemicals. However, the effect of different energy substrates on AMD treatment and microbial communities of BES remains largely unknown. Here, results showed that different energy substrates (such as glucose, acetate, ethanol, or lactate) affected the startup, maximum voltage output, power density, coulombic efficiency, and microbial communities of the microbial fuel cell (MFC). Compared with the maximum voltage output (55 mV) obtained by glucose-fed-MFC, much higher maximum voltage output (187 to 212 mV) was achieved by MFCs fed individually with other energy substrates. Acetate-fed-MFC showed the highest power density (195.07 mW/m2), followed by lactate (98.63 mW/m2), ethanol (52.02 mW/m2), and glucose (3.23 mW/m2). Microbial community analysis indicated that the microbial communities of anodic electroactive biofilms changed with different energy substrates. The unclassified_f_Enterobacteriaceae (87.48%) was predominant in glucose-fed-MFC, while Geobacter species only accounted for 0.63%. The genera of Methanobrevibacter (23.70%), Burkholderia-Paraburkholderia (23.47%), and Geobacter (11.90%) were the major genera enriched in the ethanol-fed-MFC. Geobacter was most predominant in MFC enriched by lactate (45.28%) or acetate (49.72%). Results showed that the abundance of exoelectrogens Geobacter species correlated to electricity-generation capacities of electroactive biofilms. Electroactive biofilms enriched with acetate, lactate, or ethanol effectively recovered all Cu2+ ion (349 mg/L) of simulated AMD in a cathodic chamber within 53 h by reduction as Cu0 on the cathode. However, only 34.65% of the total Cu2+ ion was removed in glucose-fed-MFC by precipitation with anions and cations rather than Cu0 on the cathode.

Effect of Nitrate Ions on Acidithiobacillus ferrooxidans-Mediated Bio-oxidation of Ferrous Ions and Pyrite

Exploring the effects of nitrate ions (NO₃^-) on the bio-oxidation of Fe²⁺ and pyrite will help reveal the actual mechanism of acid mine drainage (AMD) production. Long period shaking flask experiments were carried out in order to assess the effect of NO₃^- on the Acidithiobacillus ferrooxidans LX5 (A. ferrooxidans LX5)-mediated bio-oxidation of Fe²⁺ and pyrite. In Fe²⁺ bio-oxidation systems, A. ferrooxidans LX5 had stronger Fe²⁺ oxidation capabilities in a NO₃^--loaded solution than in a NO₃^--free solution after 24 days, and the Fe²⁺ bio-oxidation capacity of A. ferrooxidans LX5 acclimatized in solutions containing low concentrations (8.2-32.9 mmol/L) of NO₃^- was greater than when it was acclimatized in high NO₃^- concentration solutions (49.4-65.8 mmol/L). In pyrite bio-oxidation systems, in comparison with the system without NO₃^-, pyrite bio-oxidation efficiency was significantly increased when the NO₃^- concentration in the system was 8.2-16.5 mmol/L, and that the pyrite bio-oxidation efficiency in the system containing 8.2 mmol/L of NO₃^- was greater than that for the system with 16.5 mmol/L of NO₃^-. The pyrite bio-oxidation efficiency was inhibited when the NO₃^- concentration was above 32.9 mmol/L. The results from this study can be used to reveal the actual control behavior of NO₃^- on AMD production.

Recovery of Metals from Acid Mine Drainage by Bioelectrochemical System Inoculated with a Novel Exoelectrogen, Pseudomonas sp. E8

Acid mine drainage (AMD) is a typical source of environmental pollution ascribing to its characteristics of high acidity and heavy metal content. Currently, most strategies for AMD treatment merely focus on metal removal rather than metal recovery. However, bioelectrochemical system (BES) is a promising technology to simultaneously remove and recover metal ions from AMD. In this study, both cupric ion and cadmium ion in simulated AMD were effectively recovered by BES inoculated with a novel exoelectrogen, Pseudomonas sp. E8, that was first isolated from the anodic electroactive biofilm of a microbial fuel cell (MFC) in this study. Pseudomonas sp. E8 is a facultative anaerobic bacterium with a rod shape, 0.43–0.47 μm wide, and 1.10–1.30 μm long. Pseudomonas sp. E8 can agglomerate on the anode surface to form a biofilm in the single-chamber MFC using diluted Luria-Bertani (LB) medium as an energy substrate. A single-chamber MFC containing the electroactive Pseudomonas sp. E8 biofilms has a maximum output voltage of 191 mV and a maximum power density of 70.40 mW/m², which is much higher than those obtained by most other exoelectrogenic strains in the genus of Pseudomonas. Almost all the Cu²⁺ (99.95% ± 0.09%) and Cd²⁺ (99.86% ± 0.04%) in simulated AMD were selectively recovered by a microbial fuel cell (MFC) and a microbial electrolysis cell (MEC). After the treatment with BES, the high concentrations of Cu²⁺(184.78 mg/L), Cd²⁺(132.25 mg/L), and total iron (49.87 mg/L) in simulated AMD were decreased to 0.02, 0.19, and 0 mg/L, respectively. Scanning electron micrograph (SEM), energy dispersive X-ray spectrometry (EDXS) and X-ray diffraction (XRD) analysis indicate that the Cu²⁺ and Cd²⁺ in simulated AMD were selectively recovered by microbial electrochemical reduction as Cu⁰ (together with trace amounts of Cu₂O) or Cd⁰ on the cathode surface. Collectively, data suggest that Pseudomonas sp. E8 has great potential for AMD treatment and metal recovery.

Increased chalcopyrite bioleaching capabilities of extremely thermoacidophilic Metallosphaera sedula inocula by mixotrophic propagation

Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales, such as Metallosphaera sedula, are metabolically versatile and of great relevance in bioleaching. However, the impacts of extreme thermoacidophiles propagated with different energy substrates on subsequent bioleaching of refractory chalcopyrite remain unknown. Transcriptional responses underlying their different bioleaching potentials are still elusive. Here, it was first showed that M. sedula inocula propagated with typical energy substrates have different chalcopyrite bioleaching capabilities. Inoculum propagated heterotrophically with yeast extract was deficient in bioleaching; however, inoculum propagated mixotrophically with chalcopyrite, pyrite or sulfur recovered 79%, 78% and 62% copper, respectively, in 12 days. Compared with heterotrophically propagated inoculum, 937, 859 and 683 differentially expressed genes (DEGs) were identified in inoculum cultured with chalcopyrite, pyrite or sulfur, respectively, including upregulation of genes involved in bioleaching-associated metabolism, e.g., Fe²⁺ and sulfur oxidation, CO₂ fixation. Inoculum propagated with pyrite or sulfur, respectively, shared 480 and 411 DEGs with chalcopyrite-cultured inoculum. Discrepancies on repertories of DEGs that involved in Fe²⁺ and sulfur oxidation in inocula greatly affected subsequent chalcopyrite bioleaching rates. Novel genes (e.g., Msed_1156, Msed_0549) probably involved in sulfur oxidation were first identified. This study highlights that mixotrophically propagated extreme thermoacidophiles especially with chalcopyrite should be inoculated into chalcopyrite heaps at industrial scale.

Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans

Acidithiobacillus ferrooxidans is a gram-negative, autotrophic and rod-shaped bacterium. It can gain energy through the oxidation of Fe(II) and reduced inorganic sulfur compounds for bacterial growth when oxygen is sufficient. It can be used for bio-leaching and bio-oxidation and contributes to the geobiochemical circulation of metal elements and nutrients in acid mine drainage environments. The iron and sulfur oxidation pathways of A. ferrooxidans play key roles in bacterial growth and survival under extreme circumstances. Here, the electrons transported through the thermodynamically favourable pathway for the reduction to H₂O (downhill pathway) and against the redox potential gradient reduce to NAD(P)(H) (uphill pathway) during the oxidation of Fe(II) were reviewed, mainly including the electron transport carrier, relevant operon and regulation of its expression. Similar to the electron transfer pathway, the sulfur oxidation pathway of A. ferrooxidans, related genes and operons, sulfur oxidation mechanism and sulfur oxidase system are systematically discussed.