Bacterial Arsenic Metabolism and Its Role in Arsenic Bioremediation

Redox conditions and biochar pyrolysis temperature affecting As and Pb biogeochemical cycles and bacterial community of sediment from mining tailings

Despite the widespread use of biochar for soil and sediment remediation, little is known about the impact of pyrolysis temperature on the biogeochemistry of arsenic (As) and lead (Pb) and microorganisms in sediment under reducing conditions. In this study, we investigated the effects of pyrolysis temperature and the addition of glucose on the release and transformation of As and Pb, as well as their potential effects on the bacterial community in contaminated sediments. The addition of biochar altered the geochemical cycle of As, as it favors specific bacterial groups capable of changing species from As(V) to As(III) through fermentation, sulfate respiration and nitrate reduction. The carbon quality and content of N and S in solution shaped the pH and redox potential in a way that changed the microbial community, favoring Firmicutes and reducing Proteobacteria. This change played a fundamental role in the reductive dissolution of As and Pb minerals. The addition of biochar was the only efficient way to remove Pb, possibly as a function of its sorption and precipitation mechanisms. Such insights could contribute to the production or choice of high-efficiency biochar for the remediation of sediments subjected to redox conditions.

Insight into the genome of an arsenic loving and plant growth-promoting strain of Micrococcus luteus isolated from arsenic contaminated groundwater

Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).

Synthetic bacteria designed using ars operons: a promising solution for arsenic biosensing and bioremediation

The global concern over arsenic contamination in water due to its natural occurrence and human activities has led to the development of innovative solutions for its detection and remediation. Microbial metabolism and mobilization play crucial roles in the global cycle of arsenic. Many microbial arsenic-resistance systems, especially the ars operons, prevalent in bacterial plasmids and genomes, play vital roles in arsenic resistance and are utilized as templates for designing synthetic bacteria. This review novelty focuses on the use of these tailored bacteria, engineered with ars operons, for arsenic biosensing and bioremediation. We discuss the advantages and disadvantages of using synthetic bacteria in arsenic pollution treatment. We highlight the importance of genetic circuit design, reporter development, and chassis cell optimization to improve biosensors' performance. Bacterial arsenic resistances involving several processes, such as uptake, transformation, and methylation, engineered in customized bacteria have been summarized for arsenic bioaccumulation, detoxification, and biosorption. In this review, we present recent insights on the use of synthetic bacteria designed with ars operons for developing tailored bacteria for controlling arsenic pollution, offering a promising avenue for future research and application in environmental protection.

Unveiling the molecular mechanisms of arsenic tolerance and resilience in the primitive bryophyte Marchantia polymorpha L

This study addresses the pressing issue of high arsenic (As) contaminations, which poses a severe threat to various life forms in our ecosystem. Despite this prevailing concern, all organisms have developed some techniques to mitigate the toxic effects of As. Certain plants, such as bryophytes, the earliest land plants, exhibit remarkable tolerance to wide range of harsh environmental conditions, due to their inherent competence. In this study, bryophytes collected from West Bengal, India, across varying contamination levels were investigated for their As tolerance capabilities. Assessment of As accumulation potential and antioxidant defense efficiency, including SOD, CAT, APX, GPX etc. revealed Marchantia polymorpha as the most tolerant species. It exhibited highest As accumulation, antioxidative proficiency, and minimal damage. Transcriptomic analysis of M. polymorpha exposed to 40 μM As(III) for 24 and 48 h identified several early responsive differentially expressing genes (DEGs) associated with As tolerance. These includes GSTs, GRXs, Hsp20s, SULTR1;2, ABCC2 etc., indicating a mechanism involving vacuolar sequestration. Interestingly, one As(III) efflux-transporter ACR3, an extrusion pump, known to combat As toxicity was found to be differentially expressed compared to control. The SEM-EDX analysis, further elucidated the operation of As extrusion mechanism, which contributes added As resilience in M. polymorpha. Yeast complementation assay using Δacr3 yeast cells, showed increased tolerance towards As(III), compared to the mutant cells, indicating As tolerant phenotype. Overall, these findings significantly enhance our understanding of As tolerance mechanisms in bryophytes. This can pave the way for the development of genetically engineered plants with heightened As tolerance and the creation of improved plant varieties.

Microbial consortia-mediated arsenic bioremediation in agricultural soils: Current status, challenges, and solutions

Arsenic poisoning in agricultural soil is caused by both natural and man-made processes, and it poses a major risk to crop production and human health. Soil quality, agricultural production, runoff, ingestion, leaching, and absorption by plants are all influenced by these processes. Microbial consortia have become a feasible bioremediation technique in response to the urgent need for appropriate remediation solutions. These diverse microbial populations collaborate to combat arsenic poisoning in soil by facilitating mechanisms including oxidation-reduction, methylation-demethylation, volatilization, immobilization, and arsenic mobilization. The current state, problems, and remedies for employing microbial consortia in arsenic bioremediation in agricultural soils are examined in this review. Among the elements affecting their success include diversity, activity, community organization, and environmental conditions. Also, we emphasize the sensitivity and accuracy limits of existing assessment techniques. While earlier reviews have addressed a variety of arsenic remediation options, this study stands out by concentrating on microbial consortia as a viable strategy for arsenic removal and presents performance evaluation and technical problems. This work gives vital insights for tackling the major issue of arsenic pollution in agricultural soils by explaining the potential methods and components involved in microbial consortium-mediated arsenic bioremediation.

Arsenic uptake and accumulation in bean and lettuce plants at different developmental stages

The pattern of arsenic (As) uptake at different developmental stages in plants and its consequent influence on the growth of plants was investigated in bean and lettuce. Further, the human health risk from the consumption of these As-laced vegetables was determined. The irrigation water was contaminated with As at concentrations of 0.1, 0.25, and 0.5 mg/L. The As concentration in the plant parts (root, stem, leaves, and flower/fruit) was determined in bean at the young, flowering, and fruiting stages and lettuce at the young and mature stages. At the different growth stages, As had an impact on the biomass of bean and lettuce plant parts, but none of the biomass changes were significant (p>0.05). The increase in As concentration of the irrigation water elevated the As concentration of plant parts of both plants at all growth stages, with the exception of the bean fruit. The As concentration in the developmental stages was in the order: lettuce (young>mature) and bean (fruiting>young>flowering). In lettuce, the transfer factor was higher at the young stage (0.09-0.19, in the control and 0.1 mg/L As treatment), while in bean, it was highest at the flowering stage (0.09-0.41, in all treatments). In the edible part, lettuce possessed substantially elevated As concentrations (0.30, 0.61, and 1.21 mg/kg DW) compared to bean (0.008, 0.005, and 0.022 mg/kg DW) at As treatments of 0.1, 0.25, and 0.5 mg/L, respectively, and posed significant health risks at all applied As concentrations.

Rainwater input reduces greenhouse gas emission and arsenic uptake in paddy rice systems

This work aimed to test the hypothesis that rainwater-borne hydrogen peroxide (H2O2) can affect arsenic uptake by rice plants and emission of greenhouse gases in paddy rice systems. A mesocosm rice plant growth experiment, in conjunction with rainwater monitoring, was conducted to examine the effects of rainwater input on functional groups of soil microorganisms related to transformation of arsenic, carbon and nitrogen as well as various arsenic species in the soil and plant systems. The fluxes of methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) were measured during selected rainfall events. The results showed that rainwater-borne H2O2 effectively reacted with Fe2+ present in paddy soil to trigger a Fenton-like reaction to produce •OH. Both H2O2 and •OH inhibited As(V)-reducing microbes but promoted As(III)-oxidizing microbes, leading to a net increase in arsenate-As that is less phytoavailable compared to arsenite-As. This impeded uptake of soil-borne As by the rice plant roots, and consequently reduced the accumulation of As in the rice grains. The input of H2O2 into the soil caused more inhibition to methanogens than to methane-oxidizing microbes, resulting in a reduction in CH4 flux. The microbes mediating the transformation of inorganic nitrogen were also under oxidative stresses upon exposure to the rainwater-derived H2O2. And the limited conversion of NO3- to NO played a crucial role in reducing N2O emission from the paddy soils. The results also indicated that the rainwater-borne H2O2 could significantly affect other biogeochemical processes that shape the wider ecosystems, which is worth further investigations.

First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones

The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.

The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance

Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.

Rapid arsenite oxidation by Paenarthrobacter nicotinovorans strain SSBW5: unravelling the role of GlpF, aioAB and aioE genes

A novel arsenite resistant bacterial strain SSBW5 was isolated from the battery waste site of Corlim, Goa, India. This strain interestingly exhibited rapid arsenite oxidation with an accumulation of 5 mM arsenate within 24 h and a minimum inhibitory concentration (MIC) of 18 mM. The strain SSBW5 was identified as Paenarthrobacter nicotinovorans using 16S rDNA sequence analysis. Fourier-transformed infrared (FTIR) spectroscopy of arsenite-exposed cells revealed the interaction of arsenite with several important functional groups present on the cell surface, possibly involved in the resistance mechanism. Interestingly, the whole genome sequence analysis also clearly elucidated the presence of genes, such as GlpF, aioAB and aioE encoding transporter, arsenite oxidase and oxidoreductase enzyme, respectively, conferring their role in arsenite resistance. Furthermore, this strain also revealed the presence of several other genes conferring resistance to various metals, drugs, antibiotics and disinfectants. Further suggesting the probable direct or indirect involvement of these genes in the detoxification of arsenite thereby increasing its tolerance limit. In addition, clumping of bacterial cells was observed through microscopic analysis which could also be a strategy to reduce arsenite toxicity thus indicating the existence of multiple resistance mechanisms in strain SSBW5. In the present communication, we are reporting for the first time the potential of P. nicotinovorans strain SSBW5 to be used in the bioremediation of arsenite via arsenite oxidation along with other toxic metals and metalloids.

Removal of As(III) using a microorganism sustained secrete laccase-straw oxidation system

While laccase oxidation is a novel and promising method for treating arsenite-containing wastewater, the high cost and unsustainability of commercially available enzymes indicate a need to investigate more cost-effective viable alternatives. Here, a microorganism sustained secrete laccase-straw oxidation system (MLOS) was established and subsequently evaluated for the removal of As(III). MLOS showed efficient biological As(III) oxidation, with an As(III) removal efficiency reaching 99.9% at an initial As(III) concentration of 1.0 mg·L^-1. IC-AFS and XPS analysis showed that As(III) was partially oxidized to As(V), and partially As(III) adsorbed on the surface of rice straw. FTIR analysis revealed that hydroxyl, amine and amide groups were all involved in the As(III) removal process. SEM-EDS demonstrated that the surface structure of rice straw was destroyed following Comamonas testosteroni FJ17 (C. testosteroni FJ17) treatment, and the metal ions binding sites of rice straw were increased resulting in elemental arsenic being detected on the material surface. Molecular docking revealed the interaction between key residues of laccase and As(III). Laccase activity was negatively correlated with Cu(II) concentration in the As(III) oxidation. EEM showed that humic-like acids were also involved in the interaction with As(III). Overall, a MLOS derived from biomass waste has a significant potential to be developed as a green and sustainable technology for the treatment of wastewater containing As(III).

Copper removal capability and genomic insight into the lifestyle of copper mine inhabiting Micrococcus yunnanensis GKSM13

Heavy metal pollution in mining areas is a serious environmental concern. The exploration of mine-inhabiting microbes, especially bacteria may use as an effective alternative for the remediation of mining hazards. A highly copper-tolerant strain GKSM13 was isolated from the soil of the Singhbhum copper mining area and characterized for significant copper (Cu) removal potential and tolerance to other heavy metals. The punctate, yellow-colored, coccoid strain GKSM13 was able to tolerate 500 mg L^-1 Cu²⁺. Whole-genome sequencing identified strain GKSM13 as Micrococcus yunnanensis, which has a 2.44 Mb genome with 2176 protein-coding genes. The presence of putative Cu homeostasis genes and other heavy metal transporters/response regulators or transcription factors may responsible for multi-metal resistance. The maximum Cu²⁺ removal of 89.2% was achieved at a pH of 7.5, a temperature of 35.5 °C, and an initial Cu²⁺ ion concentration of 31.5 mg L^-1. Alteration of the cell surface, deposition of Cu²⁺ in the bacterial cell, and the involvement of hydroxyl, carboxyl amide, and amine groups in Cu²⁺ removal were observed using microscopic and spectroscopic analysis. This study is the first to reveal a molecular-based approach for the multi-metal tolerance and copper homeostasis mechanism of M. yunnanensis GKSM13.

Proteomic Analysis of Arsenic Resistance during Cyanide Assimilation by Pseudomonas pseudoalcaligenes CECT 5344

Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR analysis and determination of analytes in the cyanide-assimilating bacterium Pseudomonas pseudoalcaligenes CECT 5344. Several proteins encoded by two ars gene clusters and other Ars-related proteins were up-regulated by arsenite, even during cyanide assimilation. Although some proteins encoded by the cio gene cluster responsible for cyanide-insensitive respiration decreased in the presence of arsenite, the nitrilase NitC required for cyanide assimilation was unaffected, thus allowing bacterial growth with cyanide and arsenic. Two complementary As-resistance mechanisms were developed in this bacterium, the extrusion of As(III) and its extracellular sequestration in biofilm, whose synthesis increased in the presence of arsenite, and the formation of organoarsenicals such as arseno-phosphoglycerate and methyl-As. Tetrahydrofolate metabolism was also stimulated by arsenite. In addition, the ArsH2 protein increased in the presence of arsenite or cyanide, suggesting its role in the protection from oxidative stress caused by both toxics. These results could be useful for the development of bioremediation strategies for industrial wastes co-contaminated with cyanide and arsenic.

Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum

In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.

Recent advances in the bioremediation of arsenic-contaminated soils: a mini review

The carcinogenic metalloid arsenic (As), owing to its persistent behavior in elevated levels in soils, aggravates environmental and human health concerns. The current strategies used in the As decontamination involve several physical and chemical approaches. However, it involves high cost and even leads to secondary pollution. Therefore, it is quite imperative to explore methods that can eradicate As menace from the environment in an eco-friendly, efficient, and cost-competitive way. Searching for such viable alternatives leads to the option of bioremediation technology by utilizing various microorganisms, green plants, enzymes or even their integrated methods. This review is intended to give scientific and technical details about recent advances in the bioremediation strategies of As in soil. It takes into purview the extent, toxicological manifestations, pathways of As exposure and exemplifies the substantive need of bioremediation technologies such as phytoremediation and biosorption in a descriptive manner. Additionally, the paper looks into the wide potential of some plant growth promoting microorganisms (PGPMs) that improve plant growth on one hand and alleviate As toxicity on the other. Furthermore, it also makes a modest attempt to assimilate the use of nanoparticles, non-living biomass and transgenic crops which are the emerging alternative bioremediation technologies.