Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans

Different fates of Sb(III) and Sb(V) during the formation of jarosite mediated by Acidithiobacillus ferrooxidans

Secondary iron-sulfate minerals such as jarosite, which are easily formed in acid mine drainage, play an important role in controlling metal mobility. In this work, the typical iron-oxidizing bacterium Acidithiobacillus ferrooxidans ATCC 23270 was selected to synthesize jarosite in the presence of antimony ions, during which the solution behavior, synthetic product composition, and bacterial metabolism were studied. The results show that in the presence of Sb(V), Fe2+ was rapidly oxidized to Fe3+ by A. ferrooxidans and Sb(V) had no obvious effect on the biooxidation of Fe2+ under the current experimental conditions. The presence of Sb(III) inhibited bacterial growth and Fe2+ oxidation. For the group with Sb(III), products with amorphous phases were formed 72 hr later, which were mainly ferrous sulfate and pentavalent antimony oxide, and the amorphous precursor was finally transformed into a more stable crystal phase. For the group with Sb(V), the morphology and structure of jarosite were changed in comparison with those without Sb. The biomineralization process was accompanied by the removal of 94% Sb(V) to form jarosite containing the Fe-Sb-O complex. Comparative transcriptome analysis shows differential effects of Sb(III) and Sb(V) on bacterial metabolism. The expression levels of functional genes related to cell components were much more downregulated for the group with Sb(III) but much more regulated for that with Sb(V). Notably, cytochrome c and nitrogen fixation-relevant genes for the A.f_Fe2+_Sb(III) group were enhanced significantly, indicating their role in Sb(III) resistance. This study is of great value for the development of antimony pollution control and remediation technology.

Humic acid-mediated mechanism for efficient biodissolution of used lithium batteries

Resource recovery of valuable metals from spent lithium batteries is an inevitable trend for sustainable development. In this study, external regulation was used to enhance the tolerance and stability of strains in the leaching of spent lithium batteries to radically improve the bioleaching efficiency. The leaching of Li, Ni, Co and Mn increased to 100 %, 85.06 %, 74.25 % and 69.44 % respectively after targeted cultivation with HA as compared to the undomesticated strain. In the process of microbial leaching of spent lithium batteries, the metabolites in the Ⅰ, Ⅳ, and Ⅴ regions of the metabolism of the undomesticated bacterial colony had a positive correlation to the dissolution of spent lithium batteries. The metabolites of Ⅰ, Ⅱ, and Ⅴ regions were directly affected by the HA domesticated flora on the dissolution of spent lithium batteries. The excess metabolism of protein substances can significantly promote the reduction of Ni, Co, Mn leaching, and at the same time in the role of a large number of humic substances complexed the toxic metal ions in the system, to ensure the activity of the bacterial colony. It can be seen that the bacteria were domesticated by humic acid, which promoted the bacteria's own metabolism, and the super-metabolised EPS promoted the solubilisation of spent lithium batteries.

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 knockdown 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.

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.

Metals recovery from polymetallic sulfide tailings by bioleaching functional bacteria isolated with the improved 9K agar: Comparison between one-step and two-step processes

Due to the characteristics of simple process, environmental friendliness and low operating costs, biometallurgy has become a popular technology for metals recovering from low-grade ores and tailings. In order to enhance the efficiency of bioleaching functional bacteria acquisition, the 9K agar was optimized by adjusting the ratio of two solutions to achieve better and faster solidification for the functional bacteria growth and isolation. By using the improved 9K agar, six functional stains within genera of Acidithiobacillus ferriphilus, A. ferrooxidans and Leptospirillum ferrooxidans were isolated from the enrichment of acid mine drainage. After the Fe2+ oxidation ability evaluation, three strains of WT1-1, XT2-2, and YT3-1 within the three genera were selected and employed as the individual inoculum for the bioleaching from polymetallic sulfide tailings. Eventually, a maximum leaching efficiency of 58.37% Cu, 53.14% Al, 80.09% Mg, and 76.95% Zn were observed by A. ferriphilus WT1-1 after 28 d. To further improve the bioleaching efficiency, the three strains were mixed proportionally as the inoculum in both one-step and two-step bioleaching processes. Comparing to the pure cultures, the leaching efficiencies of Cu and Mg were significantly enhanced in both one- and two-steps, while no significant change in Zn. By comparing the one- and two-step processes, leaching efficiencies of Al, Mg, and Zn were higher in the one-step process, whereas Cu was observed to be higher in the two-step process. Therefore, the selection on leaching process of one or two steps should be determined based on tailings composition and target metals.

Microflow injection analysis based on modular 3D platforms and colorimetric detection for Fe(III) monitoring in a wide concentration range

A modular microflow injection analysis (microFIA) system for the determination of Fe(III) in a bioleaching reactor has been designed, developed and validated. The different modules of the analyzer (mixer, diluter, disperser and detector) were 3D-printed. Fe(III) quantification is due by measuring the color intensity of the chelate formed between Fe(III) and salicylic acid at 525 nm. The device has been designed to dilute, disperse and detect high Fe(III) concentrations in the form of an inexpensive multi-step photometric flow cell that uses an light-emitting diode (LED) as a light source and an light-dependent resistor (LDR) as a light intensity detector. This microFIA system has been shown to be suitable for automatic and continuous determination of Fe(III) in the operation of a bioreactor for the oxidation of Fe(II). The device has a good repeatability (less than 5% of coefficient of variation in the whole range of concentrations) and accuracy of around 100%. The analyzer features an exceptional wide linear range, between 25 and 6000 mg·L-1. The device was successfully applied to the determination of Fe(III) in real samples. The obtained results proved that the method is applicable for accurate, precise, rapid, and low-cost colorimetric analysis and didn't show significant differences with a conventional UV-Vis method.

Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan

Sulfur-oxidizing bacteria play a crucial role in various processes, including mine bioleaching, biodesulfurization, and treatment of sulfur-containing wastewater. Nevertheless, the pathway involved in sulfur oxidation is highly intricate, making it complete comprehension a formidable and protracted undertaking. The mechanisms of sulfur oxidation within the Acidithiobacillus genus, along with the process of energy production, remain areas that necessitate further research and elucidation. In this study, a novel strain of sulfur-oxidizing bacterium, Acidithiobacillus Ameehan, was isolated. Several physiological characteristics of the strain Ameehan were verified and its complete genome sequence was presented in the study. Besides, the first genome-scale metabolic network model (AMEE_WP1377) was reconstructed for Acidithiobacillus Ameehan to gain a comprehensive understanding of the metabolic capacity of the strain.The characteristics of Acidithiobacillus Ameehan included morphological size and an optimal growth temperature range of 37-45°C, as well as an optimal growth pH range of pH 2.0-8.0. The microbe was found to be capable of growth when sulfur and K2O6S4 were supplied as the energy source and electron donor for CO2 fixation. Conversely, it could not utilize Na2S2O3, FeS2, and FeSO4·7H2O as the energy source or electron donor for CO2 fixation, nor could it grow using glucose or yeast extract as a carbon source. Genome annotation revealed that the strain Ameehan possessed a series of sulfur oxidizing genes that enabled it to oxidize elemental sulfur or various reduced inorganic sulfur compounds (RISCs). In addition, the bacterium also possessed carbon fixing genes involved in the incomplete Calvin-Benson-Bassham (CBB) cycle. However, the bacterium lacked the ability to oxidize iron and fix nitrogen. By implementing a constraint-based flux analysis to predict cellular growth in the presence of 71 carbon sources, 88.7% agreement with experimental Biolog data was observed. Five sulfur oxidation pathways were discovered through model simulations. The optimal sulfur oxidation pathway had the highest ATP production rate of 14.81 mmol/gDW/h, NADH/NADPH production rate of 5.76 mmol/gDW/h, consumed 1.575 mmol/gDW/h of CO2, and 1.5 mmol/gDW/h of sulfur. Our findings provide a comprehensive outlook on the most effective cellular metabolic pathways implicated in sulfur oxidation within Acidithiobacillus Ameehan. It suggests that the OMP (outer-membrane proteins) and SQR enzymes (sulfide: quinone oxidoreductase) have a significant impact on the energy production efficiency of sulfur oxidation, which could have potential biotechnological 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.

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.

Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems

Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, and they are key players in the turnover of zero-valence sulfur. However, at present, the mechanism of cyclooctasulfur activation and catabolism in Campylobacterota bacteria is not clearly understood. Here, we investigated these processes in a hydrothermal vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation and reduction. Additionally, biofilms containing cells and EPS coated on sulfur particles were observed by SEM, suggesting that biofilm formation may be involved in S0 activation in Sulfurovum species. Meanwhile, several genes encoding the outer membrane proteins of OprD family were also highly expressed, and among them, gene IMZ28_RS00565 exhibited significantly high expressions by 2.53- and 7.63-fold changes under both conditions, respectively, which may play a role in sulfur uptake. However, other mechanisms could be involved in sulfur activation and uptake, as experiments with dialysis bags showed that direct contact between cells and sulfur particles was not mandatory for sulfur reduction activity, whereas cell growth via sulfur oxidation did require direct contact. This indirect reaction could be ascribed to the role of H2S and/or other thiol-containing compounds, such as cysteine and GSH, which could be produced in the culture medium during sulfur reduction. In the periplasm, the sulfur-oxidation-multienzyme complexes soxABXY1Z1 and soxCDY2Z2 are likely responsible for thiosulfate oxidation and S0 oxidation, respectively. In addition, among the four psr gene clusters encoding polysulfide reductases, only psrA3B3C3 was significantly upregulated under the sulfur reduction condition, implying its essential role in sulfur reduction. These results expand our understanding of the interactions of Campylobacterota with the zero-valence sulfur and their adaptability to deep-sea hydrothermal environments.

Microbial Interactions in a Vitamin C Industrial Fermentation System: Novel Insights and Perspectives

In industrial production, the precursor of l-ascorbic acid (L-AA, also referred to as vitamin C), 2-keto-l-gulonic acid (2-KLG), is mainly produced using a classic two-step fermentation process performed by Gluconobacter oxydans, Bacillus megaterium, and Ketogulonicigenium vulgare. In the second step of the two-step fermentation process, the microbial consortium of K. vulgare and B. megaterium is used to achieve 2-KLG production. K. vulgare can transform l-sorbose to 2-KLG, but the yield of 2-KLG is much lower in the monoculture than in the coculture fermentation system. The relationship between the two strains is too diverse to analyze and has been a hot topic in the field of vitamin C fermentation. With the development of omics technology, the relationships between the two strains are well explained; nevertheless, the cell-cell communication is unclear. In this review, based on current omics results, the interactions between the two strains are summarized, and the potential cell-cell communications between the two strains are discussed, which will shed a light on the further understanding of synthetic consortia.

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.

A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH

The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.

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.

Manganese-Oxidizing Antarctic Bacteria (Mn-Oxb) Release Reactive Oxygen Species (ROS) as Secondary Mn(II) Oxidation Mechanisms to Avoid Toxicity

Manganese (Mn) oxidation is performed through oxidative Mn-oxidizing bacteria (MnOxb) as the main bio-weathering mechanism for Mn(III/IV) deposits during soil formation. However, with an increase in temperature, the respiration rate also increases, producing Reactive Oxygen Species (ROS) as by-products, which are harmful to microbial cells. We hypothesize that bacterial ROS oxidize Mn(II) to Mn(III/IV) as a secondary non-enzymatic temperature-dependent mechanism for cell protection. Fourteen MnOxb were isolated from Antarctic soils under the global warming effect, and peroxidase (PO) activity, ROS, and Mn(III/IV) production were evaluated for 120 h of incubation at 4 °C, 15 °C, and 30 °C. ROS contributions to Mn oxidation were evaluated in Arthrobacter oxydans under antioxidant (Trolox) and ROS-stimulated (menadione) conditions. The Mn(III/IV) concentration increased with temperature and positively correlated with ROS production. ROS scavenging with Trolox depleted the Mn oxidation, and ROS-stimulant increased the Mn precipitation in A. oxydans. Increasing the Mn(II) concentration caused a reduction in the membrane potential and bacterial viability, which resulted in Mn precipitation on the bacteria surface. In conclusion, bacterial ROS production serves as a complementary non-enzymatic temperature-dependent mechanism for Mn(II) oxidation as a response in warming environments.

Engineering microbial metabolic energy homeostasis for improved bioproduction

Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.

The potentials of biofilm reactor as recourse for the recuperation of rare earth metals/elements from wastewater: a review

Wastewater is nowadays increasingly receiving global attention as a resource much more than a problem due to its potential so serve as a resource recovery channel. In this regard, wastewater is gradually been transformed from being a cesspool to a "treasure pool." Among notable resources in the treasure pool, rare earth metals/elements (REEs) warrant focal investigation, both in terms of environmental abundance and biorecovery, due to their environmental impacts. The ineffectiveness or cost intensiveness of extant physicochemical and advanced wastewater resource recovery techniques warrants the investigation of natural phenomenons in the treasure pools. Bacteria are able to cleverly secrete certain biochemicals to help trap and aggregate nutrients for their metabolism-the biofilms. In this regard, there is increased espousal of biofilm-enabled reactors, especially for the application of the recovery of invaluable feedstock in wastewater as well as other aqueous media due to high production rates and stability of cells. Furthermore, it anticipated that this technology will be translated to recovery of rare earth elements, due to their increased demand across the globe. This piece reiterates the nitty-gritty of biofilm-enhanced biorecovery and also keeps the scientific readership abreast of the multifarious aspects regarding the successful biofilm affected biorecovery of REEs at reactor scale.

Enhanced performance of microbial fuel cells with enriched ferrous iron oxidation microflora at room temperatures

Adding ferric ions (Fe³⁺) in catholyte can enhance performance of microbial fuel cells (MFCs). This work adopted biocathode with enriched Fe²⁺ oxidizing microflora to perform in situ Fe²⁺ oxidization so the MFC could operate with prolonged period with increased cell open circuit voltage (1037 mV) and maximum power density (71.8 Wm^-3 at 154 Am^-3) but with minimal needs for iron replenishment. The Fe²⁺-oxidizing microflora was very effective so the Fe³⁺/Fe²⁺ could reach high ratio, which was composed of Acidithiobacillus (73.8%), Acidiphilium (12.1%), Mycobacterium (6.92%), Sulfobacillus (2.66%), Ochrobactrum (1.30%), Alicyclobacillus (0.82%), and other minor species. The membrane transport and cell replication were shown to be their most important metabolic activities. The formation of jarosite and hydronium jarosite by Fe³⁺ and sulfate led to loss of iron ions, which should be minimized in operation.

Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans

Cyc2 is the key protein in the outer membrane of Acidithiobacillus ferrooxidans that mediates electron transfer between extracellular inorganic iron and the intracellular central metabolism. This cytochrome c is specific for iron and interacts with periplasmic proteins to complete a reversible electron transport chain. A structure of Cyc2 has not yet been characterized experimentally. Here we describe a structural model of Cyc2, and associated proteins, to highlight a plausible mechanism for the ferrous iron electron transfer chain. A comparative modeling protocol specific for trans membrane beta barrel (TMBB) proteins in acidophilic conditions (pH ~ 2) was applied to the primary sequence of Cyc2. The proposed structure has three main regimes: Extracellular loops exposed to low-pH conditions, a TMBB, and an N-terminal cytochrome-like region within the periplasmic space. The Cyc2 model was further refined by identifying likely iron and heme docking sites. This represents the first computational model of Cyc2 that accounts for the membrane microenvironment and the acidity in the extracellular matrix. This approach can be used to model other TMBBs which can be critical for chemolithotrophic microbial growth.

Removal of odors and VOCs in municipal solid waste comprehensive treatment plants using a novel three-stage integrated biofilter: Performance and bioaerosol emissions

A novel three-stage integrated biofilter (TSIBF) composed of acidophilic bacteria reaction segment (ABRS), fungal reaction segment (FRS) and heterotrophic bacteria reaction segment (HBRS) was constructed for the treatment of odors and volatile organic compounds (VOCs)from municipal solid waste (MSW) comprehensive treatment plants. The performance, counts of predominant microorganisms, and bioaerosol emissions of a full-scale TSIBF system were studied. High and stable removal efficiencies of hydrogen sulfide, ammonia and VOCs could be achieved with the TSIBF system, and the emissions of culturable heterotrophic bacteria, fungi and acidophilic sulfur bacteria were relatively low. The removal efficiencies of different odors and VOCs, emissions of culturable microorganisms, and types of predominant microorganisms were different in the ABRS, FRS and HBRS due to the differences in reaction conditions and mass transfer in each segment. The emissions of bioaerosols from the TSIBF depended on the capture of microorganisms and their volatilization from the packing. The rational segmentation, filling of high-density packings and the accumulation of the predominant functional microorganisms in each segment enhanced the capture effect of the bioaerosols, thus reducing the emissions of microorganisms from the bioreactor.

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.

Biological materials formed by Acidithiobacillus ferrooxidans and their potential applications

A variety of biological materials including schwertmannite, jarosite, iron-sulfur cluster (ISC) and magnetosomes can be produced by Acidithiobacillus ferrooxidans (A. ferrooxidans). Their possible formation mechanisms involved in iron transformation, iron transport, and electron transfer were proposed. The schwertmannite formation usually occurs under the pH of 2.0-3.51, and a lower or higher pH will promote jarosite to be produced. Available Fe2+ in the environment and the carrier proteins that can transport Fe2+ to the intracellular membranes of A. ferrooxidans play a critical role in the synthesis of magnetosomes and ISC. The potential applications of these biological materials were reviewed, including removal of heavy metal by schwertmannite, detoxification of toxic species by jarosite, the transference of electron and ripening the iron sulfur protein by ISC, and biomedical application of magnetosomes. Additionally, some perspectives for the molecular mechanisms of synthesis and regulation of these biomaterials were briefly described.

New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses

Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 andS 2 ⁢ O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidansS 2 ⁢ O 3 2 - metabolism model involves the conversion ofS 2 ⁢ O 3 2 - to SO 4 2 - , S0 andS 4 ⁢ O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - ,S 2 ⁢ O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH inS 2 ⁢ O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellularS 2 ⁢ O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result inS 2 ⁢ O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 andS 2 ⁢ O 3 2 - substrates.

Complete Genome Sequence of Acidithiobacillus Ferrooxidans YNTRS-40, a Strain of the Ferrous Iron- and Sulfur-Oxidizing Acidophile

Acidithiobacillus ferrooxidans YNTRS-40 (A. ferrooxidans) is a chemolithoautotrophic aerobic bacterium isolated from Tengchong hot springs, Yunnan Province, China, with a broad growth pH range of 1.0–4.5. This study reports the genome sequence of this strain and the information of genes related to the adaptation of diverse stresses and the oxidation of ferrous iron and sulfur. Results showed that YNTRS-40 possesses chromosomal DNA (3,209,933-bp) and plasmid DNA (47,104-bp). The complete genome of 3,257,037-bp consists of 3,349 CDS genes comprising 6 rRNAs, 52 tRNAs, and 6 ncRNAs. There are many encoded genes associated with diverse stresses adaptation and ferrous iron and sulfur oxidation such as rus operon, res operon, petI, petII, sqr, doxDA, cydAB, and cyoABCD. This work will provide essential information for further application of A. ferrooxidans YNTRS-40 in industry.

Acidithiobacillus thiooxidans and its potential application

Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.