An Oxidoreductase AioE is Responsible for Bacterial Arsenite Oxidation and Resistance

Advances in mechanism for the microbial transformation of heavy metals: implications for bioremediation strategies

Heavy metals are extensively discharged through various anthropogenic activities, resulting in an environmental risk on a global scale. In this case, microorganisms can survive in an extreme heavy metal-contaminated environment via detoxification or resistance, playing a pivotal role in the speciation, bioavailability, and mobility of heavy metals. Therefore, studies on the mechanism for the microbial transformation of heavy metals are of great importance and can provide guidance for heavy metal bioremediation. Current research studies on the microbial transformation of heavy metals mainly focus on the single oxidation, reduction and methylation pathways. However, complex microbial transformation processes and corresponding bioremediation strategies have never been clarified, which may involve the inherent physicochemical properties of heavy metals. To uncover the underlying mechanism, we reclassified heavy metals into three categories based on their biological transformation pathways, namely, metals that can be chelated, reduced or oxidized, and methylated. Firstly, we comprehensively characterized the difference in transmembrane pathways between heavy metal cations and anions. Further, biotransformation based on chelation by low-molecular-weight organic complexes is thoroughly discussed. Moreover, the progress and knowledge gaps in the microbial redox and (de)methylation mechanisms are discussed to establish a connection linking theoretical advancements with solutions to the heavy metal contamination problem. Finally, several efficient bioremediation strategies for heavy metals and the limitations of bioremediation are proposed. This review presents a solid contribution to the design of efficient microbial remediation strategies applied in the real environment.

Nitrate reduction coupling with As(III) oxidation in neutral As-contaminated paddy soil preserves nitrogen, reduces N2O emissions and alleviates As toxicity

In arsenic (As)-contaminated paddy soil, microbial-driven nitrate (NO3-) reduction coupled with arsenite (As(III)) oxidation can reduce As toxicity, but the whereabouts of NO3- remain unclear. In this study, the experiments were established using selective streptomycin (STP) and cyclohexylamine to inhibit bacterial and fungal functional responses, respectively, and metagenomic sequencing techniques were used to explain the biological mechanisms of NO3- reduction coupled with As(III) oxidation in neutral As-contaminated paddy soil. The results indicated that fungal denitrification resulted in stronger nitrous oxide (N2O) emissions (321.6 μg kg-1) than bacterial denitrification (175.9 μg kg-1) in neutral As-contaminated paddy soil, but NO3- reduction coupled with As(III) oxidation reduced the N2O emissions. Only adding STP led to ammonium (NH4+) generation (17.7 mg kg-1), and simultaneously more NH4+ appeared in NO3- reduction coupled with As(III) oxidation; this may be because it improved the electron transfer efficiency by 18.2 %. Achromobacter was involved in denitrification coupled with As(III) oxidation. Burkholderiales was responsible for NO3- reduction to NH4+ coupled with As(III) oxidation. This study provided a theoretical basis for NO3- reduction coupled with As(III) oxidation reducing N2O emissions, promoting the reduction of NO3- to NH4+, and reducing As toxicity in paddy soil.

Arsenic and Microorganisms: Genes, Molecular Mechanisms, and Recent Advances in Microbial Arsenic Bioremediation

Throughout history, cases of arsenic poisoning have been reported worldwide, and the highly toxic effects of arsenic to humans, plants, and animals are well documented. Continued anthropogenic activities related to arsenic contamination in soil and water, as well as its persistency and lethality, have allowed arsenic to remain a pollutant of high interest and concern. Constant scrutiny has eventually resulted in new and better techniques to mitigate it. Among these, microbial remediation has emerged as one of the most important due to its reliability, safety, and sustainability. Over the years, numerous microorganisms have been successfully shown to remove arsenic from various environmental matrices. This review provides an overview of the interactions between microorganisms and arsenic, the different mechanisms utilized by microorganisms to detoxify arsenic, as well as current trends in the field of microbial-based bioremediation of arsenic. While the potential of microbial bioremediation of arsenic is notable, further studies focusing on the field-scale applicability of this technology is warranted.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Indole-Acetic Acid Promotes Ammonia Removal Through Heterotrophic Nitrification, Aerobic Denitrification With Mixed Enterobacter sp. Z1 and Klebsiella sp. Z2

Mixed Enterobacter sp. Z1 and Klebsiella sp. Z2 displayed an outstanding ammonia removal capacity than using a single strain. Metabolomics, proteomics, and RNA interference analysis demonstrated that the HNAD process was closely related to indole-acetic acid (IAA). Under the cocultured conditions, the excess IAA produced by Z2 could be absorbed by Z1 to compensate for the deficiency of IAA in the cells. IAA directly induced the expression of denitrifying enzymes and further activated the IAA metabolism level, thus greatly improving the nitrogen removal ability of Z1. In turn, nitrate and nitrite induced the expression of key enzymes in the IAA pathways. Moreover, Z1 and Z2 enhanced two IAA metabolic pathways in the process of mixed removal process. The activated hydrolysis-redox pathway in Z1 reduced the oxidative stress level, and the activated decarboxylation pathway in Z2 promoted intracellular energy metabolism, which indirectly promoted the process of HNAD in the system.

Adaptation mechanisms of arsenic metabolism genes and their host microorganisms in soils with different arsenic contamination levels around abandoned gold tailings

Soil around the gold tailing due to the smelting process of wastewater and solid waste can lead to metal (loids) contamination, especially arsenic (As). Soil microorganisms have gradually evolved adaptive mechanisms in the process of long-term adaptation to As contamination. However, comprehensive investigations on As metabolism genes and their host microbial communities in soil profiles with different levels under long-term As contamination are lacking. There are selected three typical soil profiles (0-100 cm) with different metal (loids) contamination levels (L-low, M-moderate and H-high) around tailings in this research. It uses a Metagenomic approach to explore the adaptation mechanisms of arsenic metabolism genes and arsenic metabolism gene host microorganisms in both horizontal and vertical dimensions. The results showed that four categories of As metabolism genes were prevalent in soil profiles at different As contamination, with As reduction genes being the most abundant, followed by As oxidation genes, then respiration genes and methylation genes. The As metabolism genes arsBCR, aioE, arsPH, arrAB increased with the increase of metal (loid) contaminants concentration. Longitudinal arsA, arrA, aioA, arsM and acr3 increased in abundance in deep soil. Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi were the dominant phylum of As metabolism gene host microorganisms. Different concentrations of metal (loid) contamination significantly affected the distribution of host As metabolism genes. Random forest prediction identified As as the most critical driver of As metabolism genes and their host microorganisms. Overall, this study provides a reference for a comprehensive investigation of the detoxification mechanisms of As metabolism microorganisms in soil profiles with different As contamination conditions, and is important for the development of As metabolism gene host microbial strains and engineering applications of microbial technologies to manage As contamination.

Interactions with Arsenic: Mechanisms of Toxicity and Cellular Resistance in Eukaryotic Microorganisms

Arsenic (As) is quite an abundant metalloid, with ancient origin and ubiquitous distribution, which represents a severe environmental risk and a global problem for public health. Microbial exposure to As compounds in the environment has happened since the beginning of time. Selective pressure has induced the evolution of various genetic systems conferring useful capacities in many microorganisms to detoxify and even use arsenic, as an energy source. This review summarizes the microbial impact of the As biogeochemical cycle. Moreover, the poorly known adverse effects of this element on eukaryotic microbes, as well as the As uptake and detoxification mechanisms developed by yeast and protists, are discussed. Finally, an outlook of As microbial remediation makes evident the knowledge gaps and the necessity of new approaches to mitigate this environmental challenge.

Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile

Arsenic (As), a semimetal toxic for humans, is commonly associated with serious health problems. The most common form of massive and chronic exposure to As is through consumption of contaminated drinking water. This study aimed to isolate an As resistant bacterial strain to characterize its ability to oxidize As (III) when immobilized in an activated carbon batch bioreactor and to evaluate its potential to be used in biological treatments to remediate As contaminated waters. The diversity of bacterial communities from sediments of the As-rich Camarones River, Atacama Desert, Chile, was evaluated by Illumina sequencing. Dominant taxonomic groups (>1%) isolated were affiliated with Proteobacteria and Firmicutes. A high As-resistant bacterium was selected (Pseudomonas migulae VC-19 strain) and the presence of aio gene in it was investigated. Arsenite detoxification activity by this bacterial strain was determined by HPLC/HG/AAS. Particularly when immobilized on activated carbon, P. migulae VC-19 showed high rates of As(III) conversion (100% oxidized after 36 h of incubation). To the best of our knowledge, this is the first report of a P. migulae arsenite oxidizing strain that is promising for biotechnological application in the treatment of arsenic contaminated waters.

Microbes involved in arsenic mobilization and respiration: a review on isolation, identification, isolates and implications

Microorganisms play an important role in arsenic (As) cycling in the environment. Microbes mobilize As directly or indirectly, and natural/geochemical processes such as sulphate and iron reduction, oxidative sulphide mineral dissolution, arsenite (AsO₃^3-) oxidation and arsenate (AsO₄^3-) respiration further aid in As cycle in the environment. Arsenate serves as an electron donor for the microbes during anaerobic conditions in the sediment. The present work reviews the recent development in As contamination, various As-metabolizing microbes and their phylogenetic diversity, to understand the role of microbial communities in As respiration and mobilization. It also summarizes the contemporary understanding of the intricate biochemistry and molecular biology of natural As metabolisms. Some successful examples of engineered microbes by harnessing these natural mechanisms for effective remediation are also discussed. The study indicates that there is an exigent need to have a clear understanding of environmental aspects of As mobilization and subsequent oxidation-reduction by a suitable microbial consortium.

Microbial Oxidation of Arsenite: Regulation, Chemotaxis, Phosphate Metabolism and Energy Generation

Arsenic (As) is a metalloid that occurs widely in the environment. The biological oxidation of arsenite [As(III)] to arsenate [As(V)] is considered a strategy to reduce arsenic toxicity and provide energy. In recent years, research interests in microbial As(III) oxidation have been growing, and related new achievements have been revealed. This review focuses on the highlighting of the novel regulatory mechanisms of bacterial As(III) oxidation, the physiological relevance of different arsenic sensing systems and functional relationship between microbial As(III) oxidation and those of chemotaxis, phosphate uptake, carbon metabolism and energy generation. The implication to environmental bioremediation applications of As(III)-oxidizing strains, the knowledge gaps and perspectives are also discussed.

Cooperation between two strains of Enterobacter and Klebsiella in the simultaneous nitrogen removal and phosphate accumulation processes

Two strains, Enterobacter sp. Z1 and Klebsiella sp. Z2, were exhibited great capacities for heterotrophic nitrification-aerobic denitrification (HNAD) and intracellular phosphate accumulation. Strikingly, the co-cultured strains enhanced the removal efficiency of total nitrogen and phosphate, with removal efficiencies of ammonia, nitrate, nitrite and soluble phosphate of 99.64%, 99.85%, 96.94% and 66.7% respectively. Furthermore, high removal efficiencies from wastewaters with high concentrations of ammonia (over 1000 mg/L) were achieved by inoculation with the co-strains, which left residual ammonia of less than 1 mg/L within 10 h. To elucidate the mechanism of HNAD in co-strains, quantitative PCR was carried out to examine the expression levels of hydroxylamine oxidase (Hao), nitrate reductase (NapA and NarG), nitrite reductase (NirS) and polyphosphate kinase (Ppk), and the results showed that the napA2, narG and ppk genes in the strains were significantly upregulated under the co-cultured conditions and provided an explanation for the nitrogen and phosphate removal.

Genetics and proteomics analyses reveal the roles of PhoB1 and PhoB2 regulators in bacterial responses to arsenite and phosphate

In bacteria, phosphate (Pi) stress response is governed by the two-component regulatory system, sensor kinase PhoR and its cognate response regulatory protein PhoB. The arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 contains two phoB genes, phoB1 and phoB2. phoB1 is adjacent to As(III)-oxidizing genes, however, the functions of PhoB1 and PhoB2 remain unclear. Here, phoB1 and phoB2 were each deleted in-frame, and proteomics, qRT-PCR and protein-DNA interaction were performed. We found that (1) phoB1 and phoB2 were both upregulated under low Pi conditions and phoB1 was induced by As(III), but phoB2 was not; (2) deletion of phoB1 reduced As(III)-oxidizing efficiency and protein-DNA interaction analysis showed PhoB1 could interact with aioXSR promoter to regulate As(III) oxidation; (3) deletions of phoB1 or phoB2 both reduced exopolysaccharides (EPS) synthesis; and (4) PhoB1 influenced Pi uptake, As(III) oxidation, EPS synthesis, TCA cycle, energy production and stress response with As(III), and PhoB2 was associated with Pi uptake and EPS synthesis in low Pi conditions. These results showed PhoB1 and PhoB2 were both involved in Pi acquisition, PhoB1 was more important with As(III) and PhoB2 played a major role without As(III). Strain GW4 uses these two regulators to survive under low Pi and arsenic-rich environments.

Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7

Aromatic compounds and arsenic (As) often coexist in the environment. As(III)-oxidizing bacteria can oxidize the more toxic As(III) into the less toxic As(V), and As(V) is easily removed. Microorganisms with the ability to degrade aromatic compounds and oxidize arsenite [As(III)] may have strong potential to remediate co-contaminated water. In this study, a Gram-negative bacterium Hydrogenophaga sp. H7 was shown to simultaneously degrade 3-hydroxybenzoate (3-HBA) or 4-HBA (3-/4-HBA) and oxidize arsenite [As(III)] to arsenate [As(V)] during culture. Notably, the addition of As(III) enhanced the degradation rates of 3-/4-HBA, while the addition of 3-/4-HBA resulted in a slight delay in As(III) oxidation. Use of a 1% bacterial culture in combination with FeCl₃ could completely degrade 250 mg/L 3-HBA or 4-HBA and remove 400 μM As(III) from simulated lake water within 28 h. Genomic analysis revealed the presence of As(III) oxidation/resistance genes and two putative 3-/4-HBA degradation pathways (the protocatechuate 4,5-dioxygenase degradation pathway and the catechol 2,3-dioxygenase degradation pathway). Comparative proteomics suggested that strain H7 degraded 4-HBA via the protocatechuate 4,5-dioxygenase degradation pathway in the absence of As(III); however, 4-HBA could be degraded via the catechol 2,3-dioxygenase degradation pathway in the presence of As(III). In the presence of As(III), more NADH was produced by the catechol 2,3-dioxygenase degradation pathway and/or by As(III) oxidation, which explained the enhancement of bacterial 4-HBA degradation in the presence of As(III). In addition, the key gene dmpB, which encodes catechol 2,3-dioxygenase in the catechol 2,3-dioxygenase degradation pathway, was knocked out, which resulted in the disappearance of As(III)-enhanced bacterial 4-HBA degradation from the dmpB mutant strain, which further confirmed that As(III) enhancement of 4-HBA degradation was due to the utilization of the catechol 2,3-dioxygenase pathway. These discoveries indicate that Hydrogenophaga sp. H7 has promise for the application to the removal of aromatic compounds and As co-contamination and reveal the relationship between As oxidation and aromatic compound degradation.

Efflux Transporter ArsK Is Responsible for Bacterial Resistance to Arsenite, Antimonite, Trivalent Roxarsone, and Methylarsenite

Arsenic-resistant bacteria have evolved various efflux systems for arsenic resistance. Five arsenic efflux proteins, ArsB, Acr3, ArsP, ArsJ, and MSF1, have been reported. In this study, comprehensive analyses were performed to study the function of a putative major facilitator superfamily gene, arsK, and the regulation of arsK transcriptional expression in Agrobacterium tumefaciens GW4. We found that (i) arsK is located on an arsenic gene island in strain GW4. ArsK orthologs are widely distributed in arsenic-resistant bacteria and are phylogenetically divergent from the five reported arsenic efflux proteins, indicating that it may be a novel arsenic efflux transporter. (ii) Reporter gene assays showed that the expression of arsK was induced by arsenite [As(III)], antimonite [Sb(III)], trivalent roxarsone [Rox(III)], methylarsenite [MAs(III)], and arsenate [As(V)]. (iii) Heterologous expression of ArsK in an arsenic-hypersensitive Escherichia coli strain showed that ArsK was essential for resistance to As(III), Sb(III), Rox(III), and MAs(III) but not to As(V), dimethylarsenite [dimethyl-As(III)], or Cd(II). (iv) ArsK reduced the cellular accumulation of As(III), Sb(III), Rox(III), and MAs(III) but not to As(V) or dimethyl-As(III). (v) A putative arsenic regulator gene arsR2 was cotranscribed with arsK, and (vi) ArsR2 interacted with the arsR2-arsK promoter region without metalloids and was derepressed by As(III), Sb(III), Rox(III), and MAs(III), indicating the repression activity of ArsR2 for the transcription of arsK These results demonstrate that ArsK is a novel arsenic efflux protein for As(III), Sb(III), Rox(III), and MAs(III) and is regulated by ArsR2. Bacteria use the arsR2-arsK operon for resistance to several trivalent arsenicals or antimonials.IMPORTANCE The metalloid extrusion systems are very important bacterial resistance mechanisms. Each of the previously reported ArsB, Acr3, ArsP, ArsJ, and MSF1 transport proteins conferred only inorganic or organic arsenic/antimony resistance. In contrast, ArsK confers resistance to several inorganic and organic trivalent arsenicals and antimonials. The identification of the novel efflux transporter ArsK enriches our understanding of bacterial resistance to trivalent arsenite [As(III)], antimonite [Sb(III)], trivalent roxarsone [Rox(III)], and methylarsenite [MAs(III)].

Proteomics and genetic analyses reveal the effects of arsenite oxidation on metabolic pathways and the roles of AioR in Agrobacterium tumefaciens GW4

A heterotrophic arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 isolated from As(III)-rich groundwater sediment showed high As(III) resistance and could oxidize As(III) to As(V). The As(III) oxidation could generate energy and enhance growth, and AioR was the regulator for As(III) oxidase. To determine the related metabolic pathways mediated by As(III) oxidation and whether AioR regulated other cellular responses to As(III), isobaric tags for relative and absolute quantitation (iTRAQ) was performed in four treatments, GW4 (+AsIII)/GW4 (-AsIII), GW4-ΔaioR (+AsIII)/GW4-ΔaioR (-AsIII), GW4-ΔaioR (-AsIII)/GW4 (-AsIII) and GW4-ΔaioR (+AsIII)/GW4 (+AsIII). A total of 41, 71, 82 and 168 differentially expressed proteins were identified, respectively. Using electrophoretic mobility shift assay (EMSA) and qRT-PCR, 12 genes/operons were found to interact with AioR. These results indicate that As(III) oxidation alters several cellular processes related to arsenite, such as As resistance (ars operon), phosphate (Pi) metabolism (pst/pho system), TCA cycle, cell wall/membrane, amino acid metabolism and motility/chemotaxis. In the wild type with As(III), TCA cycle flow is perturbed, and As(III) oxidation and fermentation are the main energy resources. However, when strain GW4-ΔaioR lost the ability of As(III) oxidation, the TCA cycle is the main way to generate energy. A regulatory cellular network controlled by AioR is constructed and shows that AioR is the main regulator for As(III) oxidation, besides, several other functions related to As(III) are regulated by AioR in parallel.