MerP/MerT-mediated mechanism: A different approach to mercury resistance and bioaccumulation by marine bacteria

Glutathione reductase plays a role in the metabolism of methylmercury degradation in Rhodotorula mucilaginosa

Mercury pollution is a kind of heavy metal pollution with great harm and strong toxicity which exists worldwide. Some microorganisms can convert highly toxic methylmercury into inorganic mercury compounds with significantly reduced toxicity. This is an effective means of methylmercury pollution remediation. As a safe microorganism with great potential in the remediation of heavy metal pollution, Rhodotorula mucilaginosa has not been studied in the remediation of methylmercury. Here, a R. mucilaginosa strain Rm4 with high methylmercury resistance was obtained by wild-strain screening. Its minimal inhibitory concentration and minimum lethal concentration reached 3 and 6 mg/L, respectively. At the same time, Rm4 can also degrade methylmercury. Unlike the traditional microbial methylmercury degradation pathways, R. mucilaginosa's genome does not encode the organomercury lyase gene MerB. However, transcriptomic analysis revealed that the glutathione reductase of R. mucilaginosa responds to the methylmercury degradation process. Structural domain analysis and molecular docking experiments suggest that the glutathione reductase of R. mucilaginosa has the potential to directly or indirectly participate in methylmercury degradation metabolism. Metabolic indicator tests of engineered strains overexpressing the glutathione reductase encoding gene also support this notion.

IMPORTANCE

The remediation of methylmercury pollution is crucial for environmental health. The ability of Rhodotorula mucilaginosa to resist and degrade methylmercury offers a new avenue for bioremediation efforts. Understanding the metabolic pathways involved, particularly the role of glutathione reductase, enhances our knowledge of how Rhodotorula mucilaginosa responds to methylmercury and opens up new possibilities for future research in bioremediation strategies.

Mercury-Resistant Bacteria Isolated from an Estuarine Ecosystem with Detoxification Potential

Mercury pollution is a significant environmental issue, primarily resulting from industrial activities, including gold mining extraction. In this study, 333 microorganisms were tested in increasing mercury concentrations, where 158 bacteria and 14 fungi were able to grow and remain viable at concentrations over 5.0 mg/L of mercuric chloride (II). One of the bacterial strains, Stenotrophomonas sp. INV PRT0231, isolated from the mouth of the San Juan River in the Chocó region in Colombia, showed a high mercury resistance level (MIC90 of 27 ± 9 mg/L), with a removal rate of 86.9%, an absorption rate of 1.2%, and a volatilization rate of 85.7% at pH 6.0 and 30.0 °C. The FTIR analysis showed changes in the functional groups, including fatty acid chains and methyl groups, proteins, and lipopolysaccharides associated with the carboxylate group (COO-), suggesting an important role of these biomolecules and their associated functional groups as mechanisms employed by the bacterium for mercury detoxification. Our study contributes to the understanding of the mechanisms of mercury biotransformation in microbial environmental isolates to help develop bioremediation strategies to mitigate mercury pollution caused by anthropogenic activities.

Tailored bacteria tackling with environmental mercury: Inspired by natural mercuric detoxification operons

Mercury (Hg) and its inorganic and organic compounds significantly threaten the ecosystem and human health. However, the natural and anthropogenic Hg environmental inputs exceed 5000 metric tons annually. Hg is usually discharged in elemental or ionic forms, accumulating in surface water and sediments where Hg-methylating microbes-mediated biotransformation occurs. Microbial genetic factors such as the mer operon play a significant role in the complex Hg biogeochemical cycle. Previous reviews summarize the fate of environmental Hg, its biogeochemistry, and the mechanism of bacterial Hg resistance. This review mainly focuses on the mer operon and its components in detecting, absorbing, bioaccumulating, and detoxifying environmental Hg. Four components of the mer operon, including the MerR regulator, divergent mer promoter, and detoxification factors MerA and MerB, are rare bio-parts for assembling synthetic bacteria, which tackle pollutant Hg. Bacteria are designed to integrate synthetic biology, protein engineering, and metabolic engineering. In summary, this review highlights that designed bacteria based on the mer operon can potentially sense and bioremediate pollutant Hg in a green and low-cost manner.

Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136

Heavy metals, including mercury, are non-biodegradable and highly toxic to microorganisms even at low concentrations. Understanding the mechanisms underlying the environmental adaptability of microorganisms with Hg resistance holds promise for their use in Hg bioremediation. We characterized GbsMerA, a mercury reductase belonging to the mercury-resistant operon of Gelidibacter salicanalis PAMC21136, and found its maximum activity of 474.7 µmol/min/mg in reducing Hg+2. In the presence of Ag and Mn, the enzyme exhibited moderate activity as 236.5 µmol/min/mg and 69 µmol/min/mg, respectively. GbsMerA exhibited optimal activity at pH 7.0 and a temperature of 60 °C. Moreover, the crystal structure of GbsMerA and structural comparison with homologues indicated that GbsMerA contains residues, Tyr437´ and Asp47, which may be responsible for metal transfer at the si-face by providing a hydroxyl group (-OH) to abstract a proton from the thiol group of cysteine. The complex structure with NADPH indicated that Y174 in the re-face can change its side chain direction upon NADPH binding, indicating that Y174 may have a role as a gate for NADPH binding. Moreover, the heterologous host expressing GbsMerA (pGbsMerA) is more resistant to Hg toxicity when compared to the host lacking GbsMerA. Overall, this study provides a background for understanding the catalytic mechanism and Hg detoxification by GbsMerA and suggests the application of genetically engineered E. coli strains for environmental Hg removal.

Characterization of metal resistance genes carried by waterborne free-living and particle-attached bacteria in the Pearl River Estuary

Toxic metals can substantially change the bacterial community and functions thereof in aquatic environments. Herein, metal resistance genes (MRGs) are the core genetic foundation for microbial responses to the threats of toxic metals. In this study, waterborne bacteria collected from the Pearl River Estuary (PRE) were separated into the free-living bacteria (FLB) and particle-attached bacteria (PAB), and analyzed using metagenomic approaches. MRGs were ubiquitous in the PRE water and mainly related to Cu, Cr, Zn, Cd and Hg. The levels of PAB MRGs in the PRE water ranged from 8.11 × 10⁹ to 9.93 × 10¹² copies/kg, which were significantly higher than those of the FLB (p < 0.01). It could be attributed to a large bacterial population attached on the suspended particulate matters (SPMs), which was evidenced by a significant correlation between the PAB MRGs and 16S rRNA gene levels in the PRE water (p < 0.05). Moreover, the total levels of PAB MRGs were also significantly correlated with those of FLB MRGs in the PRE water. The spatial pattern of MRGs of both FLB and PAB exhibited a declining trend from the low reaches of the PR to the PRE and on to the coastal areas, which was closely related to metal pollution degree. MRGs likely carried by plasmids were also enriched on the SPMs with a range from to 3.85 × 10⁸ to 3.08 × 10¹² copies/kg. MRG profiles and taxonomic composition of the predicted MRG hosts were significantly different between the FLB and PAB in the PRE water. Our results suggested that FLB and PAB could behave differential response to heavy metals in the aquatic environments from the perspective of MRGs.

Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review

Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.

Critical review on biogeochemical dynamics of mercury (Hg) and its abatement strategies

Mercury (Hg) is among the naturally occurring heavy metal with elemental, organic, and inorganic distributions in the environment. Being considered a global pollutant, high pools of Hg-emissions ranging from >6000 to 8000 Mg Hg/year get accumulated by the natural and anthropogenic activities in the atmosphere. These toxicants have high persistence, toxicity, and widespread contamination in the soil, water, and air resources. Hg accumulation inside the plant parts amplifies the traces of toxic elements in the linking food chains, leads to Hg exposure to humans, and acts as a potential genotoxic, neurotoxic and carcinogenic entity. However, excessive Hg levels are equally toxic to the plant system and severely disrupt the physiological and metabolic processes in plants. Thus, a plausible link between Hg-concentration and its biogeochemical behavior is highly imperative to analyze the plant-soil interactions. Therefore, it is requisite to bring these toxic contaminants in between the acceptable limits to safeguard the environment. Plants efficiently incorporate or absorb the bioavailable Hg from the soil thus a constructive understanding of Hg uptake, translocation/sequestration involving specific heavy metal transporters, and detoxification mechanisms are drawn. Whereas recent investigations in biological remediation of Hg provide insights into the potential associations between the plants and microbes. Furthermore, intense research on Hg-induced antioxidants, protein networks, metabolic mechanisms, and signaling pathways is required to understand these bioremediations techniques. This review sheds light on the mercury (Hg) sources, pollution, biogeochemical cycles, its uptake, translocation, and detoxification methods with respect to its molecular approaches in plants.

Arsenic and Mercury Distribution in an Aquatic Food Chain: Importance of Femtoplankton and Picoplankton Filtration Fractions

Arsenic (As) and mercury (Hg) were examined in the Yellowstone Lake food chain, focusing on two lake locations separated by approximately 20 km and differing in lake floor hydrothermal vent activity. Sampling spanned from femtoplankton to the main fish species, Yellowstone cutthroat trout and the apex predator lake trout. Mercury bioaccumulated in muscle and liver of both trout species, biomagnifying with age, whereas As decreased in older fish, which indicates differential exposure routes for these metal(loid)s. Mercury and As concentrations were higher in all food chain filter fractions (0.1-, 0.8-, and 3.0-μm filters) at the vent-associated Inflated Plain site, illustrating the impact of localized hydrothermal inputs. Femtoplankton and picoplankton size biomass (0.1- and 0.8-μm filters) accounted for 30%-70% of total Hg or As at both locations. By contrast, only approximately 4% of As and <1% of Hg were found in the 0.1-μm filtrate, indicating that comparatively little As or Hg actually exists as an ionic form or intercalated with humic compounds, a frequent assumption in freshwaters and marine waters. Ribosomal RNA (18S) gene sequencing of DNA derived from the 0.1-, 0.8-, and 3.0-μm filters showed significant eukaryote biomass in these fractions, providing a novel view of the femtoplankton and picoplankton size biomass, which assists in explaining why these fractions may contain such significant Hg and As. These results infer that femtoplankton and picoplankton metal(loid) loads represent aquatic food chain entry points that need to be accounted for and that are important for better understanding Hg and As biochemistry in aquatic systems. Environ Toxicol Chem 2023;42:225-241. © 2022 SETAC.

Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments

The bioleaching process is carried out by aerobic acidophilic iron-oxidizing bacteria that are mainly mesophilic or moderately thermophilic. However, many mining sites are located in areas where the mean temperature is lower than the optimal growth temperature of these microorganisms. In this work, we report the obtaining and characterization of two psychrotolerant bioleaching bacterial strains from low-temperature sites that included an abandoned mine site in Chilean Patagonia (PG05) and an acid rock drainage in Marian Cove, King George Island in Antarctic (MC2.2). The PG05 and MC2.2 strains showed significant iron-oxidation activity and grew optimally at 20°C. Genome sequence analyses showed chromosomes of 2.76 and 2.84 Mbp for PG05 and MC2.2, respectively, and an average nucleotide identity estimation indicated that both strains clustered with the acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans. The Patagonian PG05 strain had a high content of genes coding for tolerance to metals such as lead, zinc, and copper. Concordantly, electron microscopy revealed the intracellular presence of polyphosphate-like granules, likely involved in tolerance to metals and other stress conditions. The Antarctic MC2.2 strain showed a high dosage of genes for mercury resistance and low temperature adaptation. This report of cold-adapted cultures of the At. ferrooxidans species opens novel perspectives to satisfy the current challenges of the metal bioleaching industry.

Draft genome sequence of Pseudomonas sp. A46 isolated from mercury-contaminated wastewater

Pseudomonas sp. A46 was first isolated from mercury-contaminated groundwater in Taiwan. This study is the first to report the draft whole-genome sequence of Pseudomonas sp. A46. Its genome consists of 126 contigs, with a total length of 6,782,516 bp and a GC content of 64.7%. Phylogenetic analysis based on 16 S rRNA gene sequences revealed that Pseudomonas sp. A46 is closely related to Pseudomonas citronellolis. Assessment of the draft genome sequence revealed that Pseudomonas sp. A46 harbors sets of genes conferring resistance to heavy metals, such as mercury, zinc, lead, copper, cadmium, chromate, and arsenate. These identified genes enable this bacterium to tolerate heavy metal stress.

Winogradskyella luteola sp.nov., Erythrobacter ani sp. nov., and Erythrobacter crassostrea sp.nov., isolated from the hemolymph of the Pacific Oyster Crassostrea gigas

Three new bacterial strains, WHY3^T, WH131^T, and WH158^T, were isolated and described from the hemolymph of the Pacific oyster Crassostrea gigas utilizing polyphasic taxonomic techniques. The 16S rRNA gene sequence analysis revealed that strain WHY3^T was a member of the genus Winogradskyella, whereas strains WHI31^T and WH158^T were members of the genus Erythrobacter. According to the polygenomic study the three strains formed individual lineages with strong bootstrap support. The comparison of dDDH-and ANI values, percentage of conserved proteins (POCP), and average amino acid identity (AAl) between the three strains and their relatives established that the three strains represented two separate genera. Menaquinone-6 was reported as the major respiratory quinone in strain WHY3^T and Ubiquinone-10 for strains WH131^T and WH158^T, respectively. The major cellular fatty acids for strain WHY3^T were C_15:0, anteiso-C_15:1 ω7c, iso-C_15:0, C_16:1ω7c. The major cellular fatty acids for strains WH131^T and WH158^T were C_14:02-OH and t_18:1ω12 for WH131^T and C_17:0, and C_18:1ω7c for strain WH158^T. Positive Sudan Black B staining Indicated the presence of polyhydroxyalkanoic acid granules for strains WH131^T and WH158^T but not for strain WHY3^T. The DNA G + C contents of strains WHY3^T, WH131^T and WH158^T were 34.4, 59.7 and 56.6%, respectively. Gene clusters predicted some important genes involved in the bioremediation process. Due to the accomplishment of polyphasic taxonomy, we propose three novel species Winogradskyella luteola sp.nov. (type strain WHY3^T = DSM 111804^T = NCCB 100833^T), Erythrobacter ani sp.nov. (WH131^T = DSM 112099^T = NCCB 100824^T) and Erythrobacter crassostrea sp.nov. (WH158^T = DSM 112102^T = NCCB 100877^T).

Mechanisms controlling the transformation of and resistance to mercury(II) for a plant-associated Pseudomonas sp. strain, AN-B15

Bioremediation using mercury (Hg)-volatilizing and immobilizing bacteria is an eco-friendly and cost-effective strategy for Hg-polluted farmland. However, the mechanisms controlling the transformation of and resistance to Hg(II) by these bacteria remain unknown. In this study, a plant-associated Pseudomonas sp. strain, AN-B15 was isolated and determined to effectively remove Hg(II) under both nutrient-poor and nutrient-rich conditions via volatilization by transforming Hg(II) to Hg(0) and immobilization by transforming Hg(II) to mercury sulfide and Hg-sulfhydryl. Genome and transcriptome analyses revealed that the molecular mechanisms involved in Hg(II) resistance in AN-B15 were a collaborative process involving multiple metabolic systems at the transcriptional level. Under Hg(II) stress, AN-B15 upregulated genes involved in the mer operon and producing the reducing power to rapidly volatilize Hg(II), thereby decreasing its toxicity. Hydroponic culture experiments also revealed that inoculation with strain AN-B15 alleviated Hg-induced toxicity and reduced the uptake of Hg(II) in the roots of wheat seedlings, as explained by the volatilization and immobilization of Hg(II) and plant growth-promoting traits of AN-B15. Overall, the results from the in vitro assays provided vital information that are essential for understanding the mechanism of Hg(II) resistance in plant-associated bacteria, which can also be applied for the bioremediation of Hg-contamination in future.

The alteration of gut microbiome community play an important role in mercury biotransformation in largemouth bass

Mercury (Hg) biotransformation is an important process that can affect the speciation and bioaccumulation of Hg in fish. The intestinal microbiota has been suggested to take part in this process. However, Hg biotransformation in fish is still unclear and the responses of gut microbiota to different Hg exposure scenarios have not been well addressed. The present study investigated the bioaccumulation and biotransformation of Hg in a freshwater fish (Micropterus salmoides) and characterized the gut microbiome community under dietary inorganic Hg (IHg) or methylmercury (MeHg) exposure, aiming to evaluate the effects of gut microbiome's activities on the internal-handling and fate of Hg in fish. Significant Hg methylation was observed in fish under IHg exposure, whereas there was no demethylation occurred in MeHg-treated fish. Both IHg and MeHg could significantly alter the community composition of gut microbiome. The administrated IHg in the food could enhance the growth of methylators, resulting in additional MeHg production in fish gut. However, abundance of demethylators was greatly decreased under either IHg or MeHg exposure, leading the demethylation process to be negligible. The results strongly suggested that the behaviors of gut bacterial community played an important role in the presence or absence of biotransformation processes. This study elucidated the importance of gut microbiome in Hg biotransformation process, and helped to develop a novel perspective to understand the Hg bioaccumulation of fish in realistic environment.

Cellular and genetic mechanism of bacterial mercury resistance and their role in biogeochemistry and bioremediation

Mercury (Hg) is a highly toxic element that occurs at low concentrations in nature. However, various anthropogenic and natural sources contribute around 5000 to 8000 metric tons of Hg per year, rapidly deteriorating the environmental conditions. Mercury-resistant bacteria that possess the mer operon system have the potential for Hg bioremediation through volatilization from the contaminated milieus. Thus, bacterial mer operon plays a crucial role in Hg biogeochemistry and bioremediation by converting both reactive inorganic and organic forms of Hg to relatively inert, volatile, and monoatomic forms. Both the broad-spectrum and narrow-spectrum bacteria harbor many genes of mer operon with their unique definitive functions. The presence of mer genes or proteins can regulate the fate of Hg in the biogeochemical cycle in the environment. The efficiency of Hg transformation depends upon the nature and diversity of mer genes present in mercury-resistant bacteria. Additionally, the bacterial cellular mechanism of Hg resistance involves reduced Hg uptake, extracellular sequestration, and bioaccumulation. The presence of unique physiological properties in a specific group of mercury-resistant bacteria enhances their bioremediation capabilities. Many advanced biotechnological tools also can improve the bioremediation efficiency of mercury-resistant bacteria to achieve Hg bioremediation.

Nickel bioaccumulation by a marine bacterium Brevibacterium sp. (X6) isolated from Shenzhen Bay, China

Nickel bioaccumulation capacity of a marine Brevibacterium sp., designated as X6, was evaluated to explore its potential application in the bioremediation of Ni²⁺ pollutants in marine environments. The minimum Ni²⁺ inhibitory concentration and maximum Ni²⁺ bioaccumulation of X6 were 1000 mg/L and 100.95 mg/g, respectively, higher than most reported strains. Among the co-existing metal ions in seawater, K⁺ caused a slight adverse impact on Ni²⁺ uptake, followed by Na⁺ and Ca²⁺, whereas Mg²⁺ drastically inhibited Ni²⁺ bioaccumulation. Other heavy metals such as Co²⁺, Zn²⁺ and Cd²⁺ moderately affected Ni²⁺ binding, but the adverse effect of Cu²⁺ was severe. The investigation of the mechanism of Ni²⁺ bioaccumulation revealed that 66.34% of the accumulated Ni²⁺ was bound to the cell surface. Carboxylic, hydroxyl, amino and thiol groups participated in Ni²⁺ binding, while carboxylic group contributed the most, while thiol group may be more involved in Ni²⁺ binding at low Ni²⁺ concentrations.

Marine Microbial Response to Heavy Metals: Mechanism, Implications and Future Prospect

Growing levels of pollution in marine environment has been a matter of serious concern in recent years. Increased levels of heavy metals due to improper waste disposal has led to serious repercussions. This has increased occurrences of heavy metals in marine fauna. Marine microbes are large influencers of nutrient cycling and productivity in oceans. Marine bacteria show altered metabolism as a strategy against metal induced stress. Understanding these strategies used to avoid toxic effects of heavy metals can help in devising novel biotechnological applications for ocean clean-up. Using biological tools for remediation has advantages as it does not involve harmful chemicals and it shows greater flexibility to environmental fluctuations. This review provides a comprehensive insight on marine microbial response to heavy metals and sheds light on existing knowledge about and paves for new avenues in research for bioremediation strategies.