Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency

Acidithiobacillus spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of A. ferridurans to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of A. ferridurans DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.

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.

The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes

IMPORTANCE

Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae, for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter. Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.

Fe/S Redox-Coupled Mercury Transformation Mediated by Acidithiobacillus ferrooxidans ATCC 23270 under Aerobic and/or Anaerobic Conditions

Bioleaching processes or microbially mediated iron/sulfur redox processes in acid mine drainage (AMD) result in mineral dissolution and transformation, the release of mercury and other heavy metal ions, and changes in the occurrence forms and concentration of mercury. However, pertinent studies on these processes are scarce. Therefore, in this work, the Fe/S redox-coupled mercury transformation mediated by Acidithiobacillus ferrooxidans ATCC 23270 under aerobic and/or anaerobic conditions was studied by combining analyses of solution behavior (pH, redox potential, and Fe/S/Hg ion concentrations), the surface morphology and elemental composition of the solid substrate residue, the Fe/S/Hg speciation transformation, and bacterial transcriptomics. It was found that: (1) the presence of Hg²⁺ significantly inhibited the apparent iron/sulfur redox process; (2) the addition of Hg²⁺ caused a significant change in the composition of bacterial surface compounds and elements such as C, N, S, and Fe; (3) Hg mainly occurred in the form of Hg⁰, HgS, and HgSO₄ in the solid substrate residues; and (4) the expression of mercury-resistant genes was higher in earlier stages of growth than in the later stages of growth. The results indicate that the addition of Hg²⁺ significantly affected the iron/sulfur redox process mediated by A. ferrooxidans ATCC 23270 under aerobic, anaerobic, and coupled aerobic-anaerobic conditions, which further promoted Hg transformation. This work is of great significance for the treatment and remediation of mercury pollution in heavy metal-polluted areas.

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.

Investigating the rus and petI operon expression patterns in exposed Acidithiobacillus ferrooxidans sp. FJ2 to different doses of gamma irradiation

The bioleaching process is developing as an economic and successful biotechnology method in the metallurgy industry. Acidithiobacillus ferrooxidans is one of the most important bacteria involved in uranium bioleaching which converts insoluble U⁴⁺ to soluble U⁶⁺ by oxidation of Fe²⁺ to Fe³⁺ using several periplasmic proteins encoded by the genes in rus and petI operons in its electron transport pathway. Accordingly, the purpose of this study was to consider the expression of these genes through exposed A. ferrooxidans sp. FJ2 to γ-ray in 17 different doses targeting uranium extraction yield. Acidithiobacillus ferrooxidans sp. FJ2 was irradiated by gamma rays at 25, 50, 75, 100, 150, 300, 450, 600, 750 Gy and 1, 2, 5, 10, 15, 20, 25 and 30 kGy doses. Moreover, the Eh value of 9k culture media was measured as special screening criteria to select the four treatments. The selected bacteria were cultured in 9k media, containing 50% uranium ore powder in the bioleaching process. Then, the value of pH & Eh of culture media, Fe²⁺ and uranium concentrations in 4, 8 and 13 day's period of incubation were measured. In followings, the expression levels of cyc1, cyc2, rus, coxB, petA, petB, petC and cycA genes at the end of each period were investigated by real-time PCR. Overall, all samples demonstrated a decrease in pH value and Fe²⁺ concentration and an increase in Eh value and U concentration in time intervals. The gamma irradiation in given doses raised the expression levels of all genes encoded in rus and petI operons, except petB gene during the bioleaching process, although, it had no effect either on the pH, Eh values or on Fe²⁺ and uranium concentrations. This result implies that during the oxidation of ferrous iron and formation of Jarosite sediment, the decreasing trend of pH and the increasing trend of Eh occurred in all samples. However, the differences in expression of the genes of rus and petI operons in the samples did not have an effect on uranium extraction.

A regulation mechanism for the promoter region of the pet II operon in Acidithiobacillus ferrooxidans ATCC23270

Acidithiobacillus ferrooxidans ATCC23270 is a gram-negative and autotrophic bacillus acquiring energy via the oxidation of iron and sulfur. The pet II operon is involved in the sulfur metabolism of A. ferrooxidans. However, the mechanisms that control the expression of the pet II operon are poorly understood. We previously described that the AFE2726 protein is associated with the expression of the pet II operon. Here, we attempted to analyze the involvement of AFE2726 in the regulation of pet II operon expression. First, pEGF recombinant vectors driven by the promotor of the pet II operon, denoted pEGF-pet II, were constructed. Then, DH5α E. coli cultures containing the vector mentioned above were cultivated in Na₂S₂O₃, as this medium substantially enhances the expression of green fluorescent proteins. To examine the regulatory effect of AFE2726 on the pet II operon, the C62/V and C72/V mutants for AFE2726 were constructed in pEGF-pet II vectors using the site-directed deletion method. Compared to pEFG-pet II and pEFG-pet II-Δ-C62/V, pEFG-pet II-Δ-C72/V reduced the expression of green fluorescent proteins dramatically when transformed into DH5α E.coli in Na₂S₂O₃ medium. This suggested that the 72nd cysteine was a crucial residue of the AFE2726 protein, affecting the response of the pet II operon to sodium thiosulfate. Furthermore, the binding site of AFE2726 on the promotor of the pet II operon was identified using the electrophoretic mobility shift assay (EMSA), and it was found to be a 34bp inverted repeat sequence (named IR4), which ranged from -65 to -32. In summary, our results indicated that the AFE2726 protein regulates the pet II operon by binding to the IR4 sequence in its promotor region, whose function is likely affected by Na₂S₂O₃ binding to its Cys72 residue counterpart.

A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans

Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respiratory model was proposed. In the model, [NiFe] hydrogenases oxidize hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated iron-sulfur proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa ₃ oxidase via cytochrome bc ₁ complex and cytochrome c ₄ or the alternate directly to cytochrome bd oxidase, resulting in proton efflux and reduction of oxygen. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferrireductase) via cytochrome bc ₁ complex and a cascade of electron transporters (cytochrome c ₄, cytochrome c ₅₅₂, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux and reduction of ferric iron. The proton gradient generated by hydrogen oxidation maintains the membrane potential and allows the generation of ATP and NADH. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition of the deep terrestrial subsurface.

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10⁸ cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

Acidithiobacillus ferrianus sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph

Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MG^T (= DSM 107098^T = JCM 33084^T). Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.

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.