Bacterial mercury resistance from atoms to ecosystems

Intestinal microbiota protects against methylmercury-induced neurotoxicity

Methylmercury (MeHg) remains a global public health issue because of its frequent presence in human food sources obtained from the water. The excretion of MeHg in humans occurs slowly with a biological half-time of 32-47 days. Short-term MeHg exposure may cause long-lasting neurotoxicity. The excretion through feces is a major route in the demethylation of MeHg. Accumulating evidence suggests that the intestinal microbiota plays an important role in the demethylation of MeHg, thereby protecting the host from neurotoxic effects. Here, we discuss recent developments on the role of intestinal microbiota in MeHg metabolism, based on in vitro cell culture experiments, experimental animal studies and human investigations. Demethylation by intestinal bacteria is the rate-limiting step in MeHg metabolism and elimination. The identity of bacteria strains responsible for this biotransformation is currently unknown; however, the non-homogenous distribution of intestinal microbiota may lead to different demethylation rates in the intestinal tract. The maintenance of intestinal barrier function by intestinal microbiota may afford protection against MeHg-induced neurotoxicity, which warrant future investigations. We also discuss studies investigating the effects of MeHg exposure on the population structural stability of intestinal microbiota in several host species. Although this is an emerging area in metal toxicity, current research suggests that a change in certain phyla in the intestinal microbiota may indicate MeHg overexposure.

Degradation of organic mercury in high salt environments by a marine aerobic bacterium Alteromonas macleodii KD01

Mercury (Hg), particularly organic mercury, poses a global concern due to its pronounced toxicity and bioaccumulation. Bioremediation of organic mercury in high-salt wastewater faces challenges due to the growth limitations imposed by elevated Cl- and Na+ concentrations on microorganisms. In this study, an isolated marine bacterium Alteromonas macleodii KD01 was demonstrated to degrade methylmercury (MeHg) efficiently in seawater and then was applied to degrade organic mercury (MeHg, ethylmercury, and thimerosal) in simulated high-salt wastewater. Results showed that A. macleodii KD01 can rapidly degrade organic mercury (within 20 min) even at high concentrations (>10 ng/mL), volatilizing a portion of Hg from the wastewater. Further analysis revealed an increased transcription of organomercury lyase (merB) with rising organic mercury concentrations during the exposure process, suggesting the involvement of mer operon (merA and merB). These findings highlight A. macleodii KD01 as a promising candidate for addressing organic mercury pollution in high-salt wastewater.

Building on a theme: The redox hierarchy of pyridine nucleotide-disulfide oxidoreductases

Flavin disulfide reductases (FDRs) are FAD-dependent enzymes that transmit electrons from NAD(P)H to reduce specific oxidant substrate disulfides. These enzymes have been studied extensively, most particularly the paradigm examples: glutathione reductase and thioredoxin reductase. The common, though not universal, traits of the family include a tyrosine- or phenylalanine-gated binding pocket for NAD(P) nicotinamides adjacent to the FAD isoalloxazine re-face, and a disulfide stacked against the si-face of the isoalloxazine whose dithiol form is activated for subsequent exchange reactions by a nearby histidine acting as a base. This arrangement promotes transduction of the reducing equivalents for disulfide exchange relay reactions. From an observational standpoint the proximal parallel stacking of three redox moieties induces up to three opportunities for unique charge transfer interactions (NAD(P)H FAD, NAD(P)+•FADH2, and FAD•thiolate). In transient state, the charge transfer transitions provide discrete signals to assign reaction sequences. This review summarizes the lineage of observations for the FDR enzymes that have been extensively studied. Where applicable and in order to chart a consistent interpretation of the record, only data derived from studies that used anaerobic methods are cited. These data reveal a recurring theme for catalysis that is elaborated with specific additional functionalities for each oxidant substrate.

Microbial assisted multifaceted amelioration processes of heavy-metal remediation: a clean perspective toward sustainable and greener future

Rapidly increasing heavy metal waste has adversely affected the environment and the Earth's health. The lack of appropriate remediation technologies has worsened the issue globally, especially in developing countries. Heavy-metals contaminants have severely impacted the environment and led to devastating conditions owing to their abundance and reactivity. As they are nondegradable, the potential risk increases even at a low concentration. However, heavy-metal remediation has increased with the up-gradation of technologies and integration of new approaches. Also, of all the treatment methodologies, microbial-assisted multifaceted approach for ameliorating heavy metals is a promising strategy for propagating the idea of a green and sustainable environment with minimal waste aggregation. Microbial remediation combined with different biotechniques could aid in unraveling new methods for eradicating heavy metals. Thus, the present review focuses on various microbial remediation approaches and their affecting factors, enabling recapitulation of the interplay between heavy-metals ions and microorganisms. Additionally, heavy-metals remediation mechanisms adapted by microorganisms, the role of genetically modified (GM) microorganisms, life cycle assessment (LCA), techno-economic assessment (TEA) limitations, and prospects of microbial-assisted amelioration of heavy-metals have been elaborated in the current review with focus toward "sustainable and greener future."

In vitro and in vivo screening of bacterial species from contaminated soil for heavy metal biotransformation activity

Heavy metals (HMs) are widely used in various industries. High concentrations of HMs can be severely toxic to plants, animals and humans. Microorganism-based bioremediation has shown significant potential in degrading and detoxifying specific HM contaminants. In this study, we cultivated a range of bacterial strains in liquid and solid nutrient medium containing different concentrations of different HMs to select and analyze bacteria capable of transforming HMs. The bacterial strains most resistant to selected HMs and exhibiting the ability to remove HMs from contaminated soils were identified. Then, the bacterial species capable of utilizing HMs in soil model experiments were selected, and their ability to transform HMs was evaluated. This study has also generated preliminary findings on the use of plants for further removal of HMs from soil after microbial bioremediation. Alcaligenes faecalis, Delftia tsuruhatensis and Stenotrophomonas sp. were selected for their ability to grow in and utilize HM ions at the maximum permissible concentration (MPC) and two times the MPC. Lysinibacillus fusiformis (local microflora) can be used as a universal biotransformation tool for many HM ions. Brevibacillus parabrevis has potential for the removal of lead ions, and Brevibacillus reuszeri and Bacillus safensis have potential for the removal of arsenic ions from the environment. The bacterial species have been selected for bioremediation to remove heavy metal ions from the environment.

Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms

In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.

Unmasking the physiology of mercury detoxifying bacteria from polluted sediments

Marine sediments polluted from anthropogenic activities can be major reservoirs of toxic mercury species. Some microorganisms in these environments have the capacity to detoxify these pollutants, by using the mer operon. In this study, we characterized microbial cultures isolated from polluted marine sediments growing under diverse environmental conditions of salinity, oxygen availability and mercury tolerance. Specific growth rates and percentage of mercury removal were measured in batch cultures for a selection of isolates. A culture affiliated with Pseudomonas putida (MERCC_1942), which contained a mer operon as well as other genes related to metal resistances, was selected as the best candidate for mercury elimination. In order to optimize mercury detoxification conditions for strain MERCC_1942 in continuous culture, three different dilution rates were tested in bioreactors until the cultures achieved steady state, and they were subsequently exposed to a mercury spike; after 24 h, strain MERCC_1942 removed up to 76% of the total mercury. Moreover, when adapted to high growth rates in bioreactors, this strain exhibited the highest specific mercury detoxification rates. Finally, an immobilization protocol using the sol-gel technology was optimized. These results highlight that some sediment bacteria show capacity to detoxify mercury and could be used for bioremediation applications.

Adsorption of Hg2+/Cr6+ by metal-binding proteins heterologously expressed in Escherichia coli

BACKGROUND

Removal of heavy metals from water and soil is a pressing challenge in environmental engineering, and biosorption by microorganisms is considered as one of the most cost-effective methods. In this study, the metal-binding proteins MerR and ChrB derived from Cupriavidus metallidurans were separately expressed in Escherichia coli BL21 to construct adsorption strains. To improve the adsorption performance, surface display and codon optimization were carried out.

RESULTS

In this study, we constructed 24 adsorption engineering strains for Hg2+ and Cr6+, utilizing different strategies. Among these engineering strains, the M'-002 and B-008 had the strongest heavy metal ion absorption ability. The M'-002 used the flexible linker and INPN to display the merRopt at the surface of the E. coli BL21, whose maximal adsorption capacity reached 658.40 μmol/g cell dry weight under concentrations of 300 μM Hg2+. And the B-008 overexpressed the chrB in the intracellular, its maximal capacity was 46.84 μmol/g cell dry weight under concentrations 500 μM Cr6+. While in the case of mixed ions solution (including Pb2+, Cd2+, Cr6+ and Hg2+), the total amount of ions adsorbed by M'-002 and B-008 showed an increase of up to 1.14- and 4.09-folds, compared to the capacities in the single ion solution.

CONCLUSION

The construction and optimization of heavy metal adsorption strains were carried out in this work. A comparison of the adsorption behavior between single bacteria and mixed bacteria systems was investigated in both a single ion and a mixed ion environment. The Hg2+ absorption capacity is reached the highest reported to date with the engineered strain M'-002, which displayed the merRopt at the surface of chassis cell, indicating the strain's potential for its application in practical environments.

Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils

Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2-8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.

Study of mercury resistance and Fourier transform infrared spectroscopy-based metabolic profiling of a potent Bacillus tropicus strain from forest soil

Mercury (Hg) is a highly toxic heavy metal and Hg-resistant indigenous bacterial isolates may offer a green and cost-effective bioremediation strategy to counter Hg contamination. In this study, a potent Hg-resistant bacterium was isolated from the forest soil of a bird sanctuary. Identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry depicted the isolate as a strain of Bacillus tropicus, validated by morphological, biochemical, and molecular studies. The isolate demonstrated biological Hg removal efficiency and capacity of 50.67% and 19.76 mg g-1 , respectively. The plasmid borne resistance determinant, merA, encoding mercuric reductase, was detected in the bacterium endowing it with effective Hg volatilization and resistance capability. A Fourier-transform infrared spectroscopic comparative metabolic profiling revealed the involvement of various functional groups like -COOH, -CH2 , -OH, PO4 - and so on, resulting in differential spectral patterns of the bacterium both in control and Hg-exposed situations. A temporal variance in metabolic signature was also observed during the early and mid-log phase of growth in the presence of Hg. The bacterium described in this study is the first indigenous Hg-resistant strain isolated from the Uttar Dinajpur region, which could be further explored and exploited as a potent bioresource for Hg remediation.

An Overview of Bacteria-Mediated Heavy Metal Bioremediation Strategies

Contamination-free groundwater is considered a good source of potable water. Even in the twenty-first century, over 90 percent of the population is reliant on groundwater resources for their lives. Groundwater influences the economical state, industrial development, ecological system, and agricultural and global health conditions worldwide. However, different natural and artificial processes are gradually polluting groundwater and drinking water systems throughout the world. Toxic metalloids are one of the major sources that pollute the water system. In this review work, we have collected and analyzed information on metal-resistant bacteria along with their genetic information and remediation mechanisms of twenty different metal ions [arsenic (As), mercury (Hg), lead (Pb), chromium (Cr), iron (Fe), copper (Cu), cadmium (Cd), palladium (Pd), zinc (Zn), cobalt (Co), antimony (Sb), gold (Au), silver (Ag), platinum (Pt), selenium (Se), manganese (Mn), molybdenum (Mo), nickel (Ni), tungsten (W), and uranium (U)]. We have surveyed the scientific information available on bacteria-mediated bioremediation of various metals and presented the data with responsible genes and proteins that contribute to bioremediation, bioaccumulation, and biosorption mechanisms. Knowledge of the genes responsible and self-defense mechanisms of diverse metal-resistance bacteria would help us to engineer processes involving multi-metal-resistant bacteria that may reduce metal toxicity in the environment.

Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals

Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.

Mercury transformations in algae, plants, and animals: The occurrence, mechanisms, and gaps

Mercury (Hg) is a global pollutant showing potent toxicity to living organisms. The transformations of Hg are critical to global Hg cycling and Hg exposure risks, considering Hg mobilities and toxicities vary depending on Hg speciation. Though currently well understood in ambient environments, Hg transformations are inadequately explored in non-microbial organisms. The primary drivers of in vivo Hg transformations are far from clear, and the impacts of these processes on global Hg cycling and Hg associated health risks are not well understood. This hinders a comprehensive understanding of global Hg cycling and the effective mitigation of Hg exposure risks. Here, we focused on Hg transformations in non-microbial organisms, particularly algae, plants, and animals. The process of Hg oxidation/reduction and methylation/demethylation in organisms were reviewed since these processes are the key transformations between the dominant Hg species, i.e., elemental Hg (Hg0), divalent inorganic Hg (IHgII), and methylmercury (MeHg). By summarizing the current knowledge of Hg transformations in organisms, we proposed the potential yet overlooked drivers of these processes, along with potential challenges that hinder a full understanding of in vivo Hg transformations. Knowledge summarized in this review would help achieve a comprehensive understanding of the fate and toxicity of Hg in organisms, providing a basis for predicting Hg cycles and mitigating human exposure.

Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens

To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.

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.

Superoxide-Mediated Extracellular Mercury Reduction by Aerobic Marine Bacterium Alteromonas sp. KD01

Microbial reduction plays a crucial role in Hg redox and the global cycle. Although intracellular Hg(II) reduction mediated by MerA protein is well documented, it is still unclear whether or how bacteria reduce Hg(II) extracellularly without its internalization. Herein, for the first time, we discovered the extracellular reduction of Hg(II) by a widely distributed aerobic marine bacterium Alteromonas sp. KD01 through a superoxide-dependent mechanism. The generation of superoxide by Alteromonas sp. KD01 was determined using 3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide and methyl cypridina luciferin analogue as probes via UV-vis and chemiluminescence detection, respectively. The results demonstrated that Hg(II) reduction was inhibited by superoxide scavengers (superoxide dismutase (SOD) and Cu(NO3)2) or inhibitors of reduced nicotinamide adenine dinucleotide (NADH) oxidoreductases. In contrast, the addition of NADH significantly improved superoxide generation and, in turn, Hg(II) reduction. Direct evidence of superoxide-mediated Hg(II) reduction was provided by the addition of superoxide using KO2 in deionized water and seawater. Moreover, we observed that even superoxide at an environmental concentration of 9.6 ± 0.5 nM from Alteromonas sp. KD01 (5.4 × 106 cells mL-1) was capable of significantly reducing Hg(II). Our findings provide a greater understanding of Hg(II) reduction by superoxide from heterotrophic bacteria and eukaryotic phytoplankton in diverse aerobic environments, including surface water, sediment, and soil.

Sulfate-reduction and methanogenesis are coupled to Hg(II) and MeHg reduction in rice paddies

Methylmercury (MeHg) produced in rice paddies is the main source of MeHg accumulation in rice, resulting in high risk of MeHg exposure to humans and wildlife. Net MeHg production is affected by Hg(II) reduction and MeHg demethylation, but it remains unclear to what extent these processes influence net MeHg production, as well as the role of the microbial guilds involved. We used isotopically labeled Hg species and specific microbial inhibitors in microcosm experiments to simultaneously investigate the rates of Hg(II) and MeHg transformations, as well as the key microbial guilds controlling these processes. Results showed that Hg(II) and MeHg reduction rate constants significantly decreased with addition of molybdate or BES, which inhibit sulfate-reduction and methanogenesis, respectively. This suggests that both sulfate-reduction and methanogenesis are important processes controlling Hg(II) and MeHg reduction in rice paddies. Meanwhile, up to 99% of MeHg demethylation was oxidative demethylation (OD) under the incubation conditions, suggesting that OD was the main MeHg degradative pathway in rice paddies. In addition, [202Hg(0)/Me202Hg] from the added 202Hg(NO3)2 was up to 13.9%, suggesting that Hg(II) reduction may constrain Hg(II) methylation in rice paddies at the abandoned Hg mining site. This study improves our understanding of Hg cycling pathways in rice paddies, and more specifically how reduction processes affect net MeHg production and related microbial metabolisms.

Direct Uptake and Intracellular Dissolution of HgS Nanoparticles: Evidence from a Bacterial Biosensor Approach

Mercury sulfide nanoparticles (HgSNPs), which occur widely in oxic and anoxic environments, can be microbially converted to highly toxic methylmercury or volatile elemental mercury, but it remains challenging to assess their bioavailability. In this study, an Escherichia coli-based whole-cell fluorescent biosensor was developed to explore the bioavailability and microbial activation process of HgSNPs. Results show that HgSNPs (3.17 ± 0.96 nm) trigger a sharp increase in fluorescence intensity of the biosensor, with signal responses almost equal to that of ionic Hg (Hg(II)) within 10 h, indicating high bioavailability of HgSNP. The intracellular total Hg (THg) of cells exposed to HgSNPs (200 μg L-1) was 3.52-8.59-folds higher than that of cells exposed to Hg(II) (200 μg L-1), suggesting that intracellular HgSNPs were only partially dissolved. Speciation analysis using size-exclusion chromatography (SEC)-inductively coupled plasma mass spectrometry (ICP-MS) revealed that the bacterial filtrate was not responsible for HgSNP dissolution, suggesting that HgSNPs entered cells in nanoparticle form. Combined with fluorescence intensity and intracellular THg analysis, the intracellular HgSNP dissolution ratio was estimated at 22-29%. Overall, our findings highlight the rapid internalization and high intracellular dissolution ratio of HgSNPs by E. coli, and intracellular THg combined with biosensors could provide innovative tools to explore the microbial uptake and dissolution of HgSNPs.

Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain

Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.

Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury

The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe3+/Fe2+), ammonium salt (NH4+), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.

Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice

The risk of methylmercury (MeHg) toxicity following ingestion of contaminated foodstuffs (e.g., fish) is directly related to the kinetics of MeHg elimination among individuals. Yet, the factors driving the wide range of inter-individual variability in MeHg elimination within a population are poorly understood. Here, we investigated the relationship between MeHg elimination, gut microbiome demethylation activity, and gut microbiome composition using a coordinated human clinical trial and gnotobiotic mouse modeling approach together with metagenomic sequence analysis. We first observed MeHg elimination half-lives (t1/2) ranging from 28 to 90 days across 27 volunteers. Subsequently, we found that ingestion of a prebiotic induced changes in the gut microbiome and mixed effects (increased, decrease, and no effect) on elimination in these same individuals. Nonetheless, elimination rates were found to correlate with MeHg demethylation activity in cultured stool samples. In mice, attempts to remove the microbiome via generation of germ-free (GF) animals or through antibiotic (Abx) treatment both diminished MeHg demethylation to a similar extent. While both conditions substantially slowed elimination, Abx treatment resulted in significantly slower elimination than the GF condition, indicating an additional role for host-derived factors in supporting elimination. Human fecal microbiomes transplanted to GF mice restored elimination rates to that seen in control mice. Metagenomic sequence analysis of human fecal DNA did not identify genes encoding proteins typically involved in demethylation (e.g., merB, organomercury lyase). However, the abundance of several anaerobic taxa, notably Alistipes onderdonkii, were positively correlated with MeHg elimination. Surprisingly, mono-colonization of GF free mice with A. onderdonkii did not restore MeHg elimination to control levels. Collectively, our findings indicate the human gut microbiome uses a non-conventional pathway of demethylation to increase MeHg elimination that relies on yet to be resolved functions encoded by the gut microbes and the hostClinical Trial NCT04060212, prospectively registered 10/1/2019.

Conjugative Plasmid pPPUT-Tik1-1 from a Permafrost Pseudomonas putida Strain and Its Present-Day Counterparts Inhabiting Environments and Clinics

A novel group of conjugative plasmids of Pseudomonas is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of P. putida Tik1, carries a defective mercury transposon, Tn501, and a streptomycin resistance transposon, Tn5393. Ten plasmids and 34 contigs with backbone regions closely related to pPPUT-Tik1-1 have been found in GenBank. Two of these plasmids from clinical strains of P. putida and P. fulva are almost identical to the ancient plasmid. A characteristic feature of this group of plasmids is the presence of two genes encoding the initiators of replication (repA1 and repA2). None of these genes have high similarity with plasmid replication genes belonging to known incompatibility groups. It has been demonstrated that while pPPUT-Tik1-1-like plasmids have homologous backbone regions, they significantly differ by the molecular structure and the predicted functions of their accessory regions. Some of the pPPUT-Tik1-1-related plasmids carry determinants of antibiotic resistance and/or heavy metal salts. Some plasmids are characterized by the ability to degrade xenobiotics. Plasmids related to pPPUT-Tik1-1 are characterized by a narrow host range and are found in various species of the Pseudomonas genus. Interestingly, we also found shorter plasmid variants containing the same replication module, but lacking conjugation genes and containing other structural changes that strongly distinguish them from plasmids related to pPPUT-Tik1-1, indicating that the structure of the replication module cannot be used as the sole criterion for classifying plasmids. Overall, the results suggest that the plasmids of the novel group can be spread using conjugation in environmental and clinical strains of Pseudomonas and may play diverse adaptive functions due to the presence of various accessory regions.

Multidimensional Drivers of Mercury Distribution in Global Surface Soils: Insights from a Global Standardized Field Survey

Soil stores a large amount of mercury (Hg) that has adverse effects on human health and ecosystem safety. Significant uncertainties still exist in revealing environmental drivers of soil Hg accumulation and predicting global Hg distribution owing to the lack of field data from global standardized analyses. Here, we conducted a global standardized field survey and explored a holistic understanding of the multidimensional environmental drivers of Hg accumulation in global surface soils. Hg content in surface soils from our survey ranges from 3.8 to 618.2 μg kg-1 with an average of 74.0 μg kg-1 across the globe. Atmospheric Hg deposition, particularly vegetation-induced elemental Hg0 deposition, is the major source of surface soil Hg. Soil organic carbon serves as the major substrate for sequestering Hg in surface soils and is significantly influenced by agricultural management, litterfall, and elevation. For human activities, changing land-use could be a more important contributor than direct anthropogenic emissions. Our prediction of a new global Hg distribution highlights the hot spots (high Hg content) in East Asia, the Northern Hemispheric temperate/boreal regions, and tropical areas, while the cold spots (low Hg content) are in arid regions. The holistic understanding of multidimensional environmental drivers helps to predict the Hg distribution in global surface soils under a changing global environment.

Genomic Analyses of Longitudinal Mycobacterium abscessus Isolates in a Multicenter Cohort Reveal Parallel Signatures of In-Host Adaptation

BACKGROUND

Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and an increasingly frequent cause of opportunistic infections. Mycobacterium abscessus complex (MABC) is one of the major NTM lung pathogens that disproportionately colonize and infect the lungs of individuals with cystic fibrosis (CF). MABC infection can persist for years, and antimicrobial treatment is frequently ineffective.

METHODS

We sequenced the genomes of 175 isolates longitudinally collected from 30 patients with MABC lung infection. We contextualized our cohort amidst the broader MABC phylogeny and investigated genes undergoing parallel adaptation across patients. Finally, we tested the phenotypic consequences of parallel mutations by conducting antimicrobial resistance and mercury-resistance assays.

RESULTS

We identified highly related isolate pairs across hospital centers with low likelihood of transmission. We further annotated nonrandom parallel mutations in 22 genes and demonstrated altered macrolide susceptibility co-occurring with a nonsynonymous whiB1 mutation. Finally, we highlighted a 23-kb mercury-resistance plasmid whose loss during chronic infection conferred phenotypic susceptibility to organic and nonorganic mercury compounds.

CONCLUSIONS

We characterized parallel genomic processes through which MABC is adapting to promote survival within the host. The within-lineage polymorphisms we observed have phenotypic effects, potentially benefiting fitness in the host at the putative detriment of environmental survival.

Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies

The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.

The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils

Mercury (Hg) pollution is a global issue due to the high toxicity and wide dispersion of Hg around the world. Whether due to anthropogenic activities or natural processes, Hg emissions are steadily increasing, with very high levels in some regions, directly threatening human and ecosystem health. However, bacteria and fungi have evolved and adapted in response to Hg-induced stress and have developed tolerance mechanisms, notably based on the mer operon system that is involved in Hg uptake and biovolatilization via Hg reduction reactions. Other processes, such as bioaccumulation or extracellular sequestration, are involved in Hg resistance, and the study of contaminated soils has allowed the isolation of a number of microorganisms capable of these mechanisms, with strong potential for the implementation of bioremediation approaches. In addition to playing an important role in determining the fate of Hg in the biogeochemical cycle, these microorganisms can indeed be applied to reduce Hg concentrations or at least stabilize Hg for the remediation of polluted soils. Moreover, thanks to the development of biotechnological tools, bioremediation based on Hg-tolerant microorganisms can be optimized. Finally, these microorganisms are relevant candidates for biomonitoring, for example, through the engineering of biosensors, because the detection of Hg is a major issue in preserving the health of living beings.

Challenges and strategies for preventing intestinal damage associated to mercury dietary exposure

Food represents the major risk factor for exposure to mercury in most human populations. Therefore, passage through the gastrointestinal tract plays a fundamental role in its entry into the organism. Despite the intense research carried out on the toxicity of Hg, the effects at the intestinal level have received increased attention only recently. In this review we first provide a critical appraisal of the recent advances on the toxic effects of Hg at the intestinal epithelium. Next, dietary strategies aimed to diminish Hg bioavailability or modulate the epithelial and microbiota responses will be revised. Food components and additives, including probiotics, will be considered. Finally, limitations of current approaches to tackle this problem and future lines of research will be discussed.

Bioaccumulation and Bioremediation of Heavy Metals in Fishes-A Review

Heavy metals, the most potent contaminants of the environment, are discharged into the aquatic ecosystems through the effluents of several industries, resulting in serious aquatic pollution. This type of severe heavy metal contamination in aquaculture systems has attracted great attention throughout the world. These toxic heavy metals are transmitted into the food chain through their bioaccumulation in different tissues of aquatic species and have aroused serious public health concerns. Heavy metal toxicity negatively affects the growth, reproduction, and physiology of fish, which is threatening the sustainable development of the aquaculture sector. Recently, several techniques, such as adsorption, physio-biochemical, molecular, and phytoremediation mechanisms have been successfully applied to reduce the toxicants in the environment. Microorganisms, especially several bacterial species, play a key role in this bioremediation process. In this context, the present review summarizes the bioaccumulation of different heavy metals into fishes, their toxic effects, and possible bioremediation techniques to protect the fishes from heavy metal contamination. Additionally, this paper discusses existing strategies to bioremediate heavy metals from aquatic ecosystems and the scope of genetic and molecular approaches for the effective bioremediation of heavy metals.

Dissolved gaseous mercury production and sea-air gaseous exchange in impacted coastal environments of the northern Adriatic Sea

The northern Adriatic Sea is well known for mercury (Hg) contamination mainly due to historical Hg mining which took place in Idrija (Slovenia). The formation of dissolved gaseous mercury (DGM) and its subsequent volatilisation can reduce the amount of Hg available in the water column. In this work, the diurnal patterns of both DGM production and gaseous Hg fluxes at the water-air interface were seasonally evaluated in two selected environments within this area, a highly Hg-impacted, confined fish farm (VN: Val Noghera, Italy) and an open coastal zone less impacted by Hg inputs (PR: Bay of Piran, Slovenia). A floating flux chamber coupled with real-time Hg⁰ analyser was used for flux estimation in parallel with DGM concentrations determination through in-field incubations. Substantial DGM production was observed at VN (range = 126.0-711.3 pg L^-1) driven by both strong photoreduction and possibly dark biotic reduction, resulting in higher values in spring and summer and comparable concentrations throughout both day and night. Significantly lower DGM was observed at PR (range = 21.8-183.4 pg L^-1). Surprisingly, comparable Hg⁰ fluxes were found at the two sites (range VN = 7.43-41.17 ng m^-2 h^-1, PR = 0-81.49 ng m^-2 h^-1), likely due to enhanced gaseous exchanges at PR thanks to high water turbulence and to the strong limitation of evasion at VN by water stagnation and expected high DGM oxidation in saltwater. Slight differences between the temporal variation of DGM and fluxes indicate that Hg evasion is more controlled by factors such as water temperature and mixing conditions than DGM concentrations alone. The relative low Hg losses through volatilisation at VN (2.4-4.6% of total Hg) further confirm that static conditions in saltwater environments negatively affect the ability of this process in reducing the amount of Hg retained in the water column, therefore potentially leading to a greater availability for methylation and trophic transfer.

The Genome of Varunaivibrio sulfuroxidans Strain TC8T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea

Varunaivibrio sulfuroxidans type strain TC8^T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.

Mercury stable isotopes in the ocean: Analytical methods, cycling, and application as tracers

Mercury (Hg) has seven stable isotopes that can be utilized to trace the sources of Hg and evaluate the importance of transport and transformation processes in the cycling of Hg in the environment. The ocean is an integral part of the Earth and plays an important role in the global mercury cycle. However, there is a lack of a systematic review of Hg stable isotopes in marine environments. This review is divided into four sections: a) advances in Hg stable isotope analysis, b) the isotope ratios of Hg in various marine environmental matrices (seawater, sediment, and organisms), c) processes governing stable Hg isotope ratios in the ocean, and d) application of Hg stable isotopes to understand biotic uptake and migration. Mercury isotopes have provided much useful information on marine Hg cycling that cannot be given by Hg concentrations alone. This includes (i) sources of Hg in coastal or estuarine environments, (ii) transformation pathways and mechanisms of different forms of Hg in marine environments, (iii) trophic levels and feeding guilds of marine fish, and (iv) migration/habitat changes of marine fish. With the improvement of methods for seawater Hg isotope analysis (especially species-specific methods) and the measurement of Hg isotope fractionation during natural biogeochemical processes in the ocean, Hg stable isotopes will advance our understanding of the marine Hg cycle in the future, e.g., mercury exchange at the sea-atmosphere interface and seawater-sediment interface, contributions of different water masses to Hg in the ocean, fractionation mechanisms of Hg and MeHg transformation in seawater.

Capacity, stability and energy requirement of divalent mercury uptake by non-methylating/non-demethylating bacteria

Methylmercury (MeHg) uptake by demethylating bacteria and inorganic divalent mercury [Hg(II)] uptake by methylating bacteria have been extensively investigated because uptake is the initial step of the intracellular Hg transformation. However, MeHg and Hg(II) uptake by non-methylating/non-demethylating bacteria is overlooked, which may play an important role in the biogeochemical cycling of mercury concerning their ubiquitous presence in the environment. Here we report that Shewanella oneidensis MR-1, a model strain of non-methylating/non-demethylating bacteria, can take up and immobilize MeHg and Hg(II) rapidly without intracellular transformation. In addition, when taken up into MR-1 cells, the intracellular MeHg and Hg(II) were proved to be hardly exported over time. In contrast, adsorbed mercury on cell surface was observed to be easily desorbed or remobilized. Moreover, inactivated MR-1 cells (starved and CCCP-treated) were still capable of taking up nonnegligible amounts of MeHg and Hg(II) over an extended period in the absence and presence of cysteine, suggesting that active metabolism may be not required for both MeHg and Hg(II) uptake. Our results provide an improved understanding of divalent mercury uptake by non-methylating/non-demethylating bacteria and highlight the possible broader involvement of these bacteria in mercury cycling in natural environments.

Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels

Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.

Advances in bacterial whole-cell biosensors for the detection of bioavailable mercury: A review

Mercury (Hg) and its organic compounds, especially monomethylmercury (MeHg), cause major damage to the ecosystem and human health. In surface water or sediments, microorganisms play a crucial role in the methylation and demethylation of Hg. Given that Hg transformation processes are intracellular reactions, accurate assessment of the bioavailability of Hg(II)/MeHg in the environment, particularly for microorganisms, is of major importance. Compared with traditional analytical methods, bacterial whole-cell biosensors (BWCBs) provide a more accurate, convenient, and cost-effective strategy to assess the environmental risks of Hg(II)/MeHg. This Review summarizes recent progress in the application of BWCBs in the detection of bioavailable Hg(II)/MeHg, providing insight on current challenges and strategies. The principle and components of BWCBs for Hg(II)/MeHg bioavailability analysis are introduced. Furthermore, the impact of water chemical factors on the bioavailability of Hg is discussed as are future perspectives of BWCBs in bioavailable Hg analysis and optimization of BWCBs.

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.

Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation

Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km² in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.

Toward efficient bioremediation of methylmercury in sediment using merB overexpressed Escherichia coli

Sediment is the primary hotspot for microbial production of toxic and bio-accumulative methylmercury (MeHg). Common remediation strategies such as sediment dredging and capping can be too expensive and cannot degrade MeHg efficiently. Here, we constructed an Escherichia coli strain overexpressing merB gene (DH5α J23106) and assessed the effectiveness of this recombinant strain in degradation of MeHg in culture medium and sediment. DH5α J23106 can efficiently degrade MeHg (with initial concentration from 0.01 to 50 ng/mL) to more than 81.6% in a culture medium under anoxic and oxic conditions. Enriched isotope addition (¹⁹⁹HgCl₂) revealed that this recombinant strain can degrade 78.6% of newly produced Me¹⁹⁹Hg in actual sediment, however the biodegradation decreased to 36.3% for intrinsic MeHg. Degradation of spiked MeHg after aging in anoxic and oxic sediments further demonstrated DH5α J23106 can efficiently degrade newly produced MeHg and the degradation decreased with aging significantly, especially for oxic sediment. Eight sediments were further assessed for the biodegradation of aged MeHg by DH5α J23106 under oxic conditions, with degradation ratios ranging from 9.0% to 66.9%. When combined with (NH₄)₂S₂O₃ leaching, the degradation of MeHg increased by 15.8-38.8% in on-site and off-site modes through enhanced MeHg bioavailability in some of these sediments. Thus, this recombinant strain DH5α J23106 can degrade MeHg efficiently and have the potential for remediating bioavailable MeHg in contaminated sediments.

Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas

Two facultatively anaerobic, chemoorganoheterotrophic bacterial strains, designated JR1/69-2-13^T and JR1/69-3-13^T, were isolated from nitrate- and radionuclide-contaminated groundwater (Ozyorsk town, South Urals, Russia). Both strains were found to be motile, Gram-stain negative rod-shaped neutrophilic, psychrotolerant bacteria that grow within the temperature range from 5-10 to 33 °C at 0-3 (0-5)% NaCl (w/v). The major cellular fatty acids were identified as C_16:0, C_16:1 ω7c, C_18:1 ω7c and C_17:0 cyclo. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and unidentified aminophospholipids. The genomic G + C content of strains JR1/69-2-13^T and JR1/69-3-13^T was determined to be 57.2 and 57.9%, respectively. The 16S rRNA gene sequences of the strains showed high similarity between each other (98.6%) and to members of the genera Pusillimonas (96.8-98.4%) and Candidimonas (97.1-98.0%). The average nucleotide identity and digital DNA-DNA hybridization (dDDH) values among genomes of the new isolates and Pusillimonas and Candidimonas genomes were below 84.5 and 28.8%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic and chemotaxonomic characterisation, we propose assignment of strains JR1/69-3-13^T (= VKM B-3223^T = KCTC 62615^T) and JR1/69-2-13^T (= VKM B-3222^T = KCTC 62614^T) to a new genus Pollutimonas as the type strains of two new species, Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., respectively. As a result of the taxonomic revision of the genus Pusillimonas, three novel genera, Allopusillimonas, Neopusillimonas, and Mesopusillimonas are also proposed; and Candidimonas bauzanensis is reclassified as Pollutimonas bauzanensis comb. nov. Genome analysis of the new isolates suggested molecular mechanisms of their adaptation to an environment highly polluted with nitrate and radionuclides.

Seasonal changes in total mercury and methylmercury in subtropical decomposing litter correspond to the abundances of nitrogen-fixing and methylmercury-degrading bacteria

Previous research has found total mercury (THg) and methylmercury (MeHg) levels increase with litterfall decay, thus suggesting litterfall decomposition plays an essential role in the biogeochemical transformation of mercury (Hg). However, it remains unclear how Hg accumulates in the decaying litter, how bacterial taxa networks vary and what roles various microorganisms play during litterfall decomposition, especially nitrogen (N)-fixing, MeHg-degrading and Hg-methylating microbes. Here, we demonstrated as degradation proceeded, a gradually-complex network evolved for litterfall bacteria for the subtropical mixed broadleaf-conifer (MBC) forest, whereas a relatively static network existed for the evergreen broadleaf (EB) forest. N-fixing and MeHg-degrading bacteria dominated throughout litterfall decomposition process, with relative abundances of N-fixing genera and nifH copies maximum and relative abundances of MeHg-degrading bacteria and merAB copies minimum in summer. Hence, N-fixing bacteria likely mediate THg increase in the decomposing litterfall, while MeHg enhancement may be regulated by aerobic MeHg-degrading microbes which can transform MeHg to inorganic divalent Hg (Hg²⁺) or further to elemental Hg (Hg⁰). Together, this work elucidates variations of N-fixing and MeHg-degrading microbes in decaying litterfall and their relationships with Hg accumulation, providing novel insights into understanding the biogeochemical cycle of Hg in the forest ecosystem.

Structural Analyses of the Multicopper Site of CopG Support a Role as a Redox Enzyme

Metal ions can be both essential components of cells as well as potential toxins if present in excess. Organisms utilize a variety of protein systems to maintain the concentration of metal ions within the appropriate range for cellular function, and to avoid concentrations where cellular damage can occur. In bacteria, numerous proteins contribute to copper homeostasis, including copper transporters, chelators, and redox enzymes. The genes that encode these proteins are often found in clusters, thus providing modular components that work together to achieve homeostasis. A better understanding of how these components function and cooperate to achieve metal ion resistance is needed, given the extensive use of metal ions, including copper, as broad-spectrum biocides in a variety of clinical and environmental settings. The copG gene is a common component of such copper resistance clusters, but its contribution to copper resistance is not well understood. In this review the available information about the CopG protein encoded by this gene is summarized. Comparison of the recent structure to diverse copper-containing metallochaperones, metalloenzymes, and electron transfer proteins suggests that CopG is a redox enzyme that uses multiple copper ions as active site redox cofactors to act on additional copper ion substrates. Mechanisms for both oxidase and reductase activity are proposed, and the biological advantages that these activities can contribute in conjunction with existing systems are described.

Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

BACKGROUND

In our previous study, Citrobacter sp. XT1-2-2 was isolated from high cadmium-contaminated soils, and demonstrated an excellent ability to decrease the bioavailability of cadmium in the soil and inhibit cadmium uptake in rice. In addition, the strain XT1-2-2 could significantly promote rice growth and increase rice biomass. Therefore, the strain XT1-2-2 shows great potential for remediation of cadmium -contaminated soils. However, the genome sequence of this organism has not been reported so far.  RESULTS: Here the basic characteristics and genetic diversity of the strain XT1-2-2 were described, together with the draft genome and comparative genomic results. The strain XT1-2-2 is 5040459 bp long with an average G + C content of 52.09%, and contains a total of 4801 genes. Putative genomic islands were predicted in the genome of Citrobacter sp. XT1-2-2. All genes of a complete set of sulfate reduction pathway and various putative heavy metal resistance genes in the genome were identified and analyzed.

CONCLUSIONS

These analytical results provide insights into the genomic basis of microbial immobilization of heavy metals.

Metabolic engineering of the carotenoid biosynthetic pathway toward a specific and sensitive inorganic mercury biosensor

The toxicity of mercury (Hg) mainly depends on its form. Whole-cell biosensors respond selectively to toxic Hg(ii), efficiently transformed by environmental microbes into methylmercury, a highly toxic form that builds up in aquatic animals. Metabolically engineered Escherichia coli (E. coli) have successfully produced rainbow colorants. By de novo reconstruction of the carotenoid synthetic pathway, the Hg(ii)-responsive production of lycopene and β-carotene enabled programmed E. coli to potentially become an optical biosensor for the qualitative and quantitative detection of ecotoxic Hg(ii). The red color of the lycopene-based biosensor cell pellet was visible upon exposure to 49 nM Hg(ii) and above. The orange β-carotene-based biosensor responded to a simple colorimetric assay as low as 12 nM Hg(ii). A linear response was observed at Hg(ii) concentrations ranging from 12 to 195 nM. Importantly, high specificity and good anti-interference capability suggested that metabolic engineering of the carotenoid biosynthesis was an alternative to developing a visual platform for the rapid analysis of the concentration and toxicity of Hg(ii) in environmentally polluted water.

Arctic methylmercury cycling

Anthropogenic mercury (Hg) undergoes long-range transport to the Arctic where some of it is transformed into methylmercury (MeHg), potentially leading to high exposure in some Arctic inhabitants and wildlife. The environmental exposure of Hg is determined not just by the amount of Hg entering the Arctic, but also by biogeochemical and ecological processes occurring in the Arctic. These processes affect MeHg uptake in biota by regulating the bioavailability, methylation and demethylation, bioaccumulation and biomagnification of MeHg in Arctic ecosystems. Here, we present a new budget for pools and fluxes of MeHg in the Arctic and review the scientific advances made in the last decade on processes leading to environmental exposure to Hg. Methylation and demethylation are key processes controlling the pool of MeHg available for bioaccumulation. Methylation of Hg occurs in diverse Arctic environments including permafrost, sediments and the ocean water column, and is primarily a process carried out by microorganisms. While microorganisms carrying the hgcAB gene pair (responsible for Hg methylation) have been identified in Arctic soils and thawing permafrost, the formation pathway of MeHg in oxic marine waters remains less clear. Hotspots for methylation of Hg in terrestrial environments include thermokarst wetlands, ponds and lakes. The shallow sub-surface enrichment of MeHg in the Arctic Ocean, in comparison to other marine systems, is a possible explanation for high MeHg concentrations in some Arctic biota. Bioconcentration of aqueous MeHg in bacteria and algae is a critical step in the transfer of Hg to top predators, which may be dampened or enhanced by the presence of organic matter. Variable trophic position has an important influence on MeHg concentrations among populations of top predator species such as ringed seal and polar bears distributed across the circumpolar Arctic. These scientific advances highlight key processes that affect the fate of anthropogenic Hg deposited to Arctic environments.

An Extremely Stable Interprotein Tetrahedral Hg(Cys)4 Core Forms in the Zinc Hook Domain of Rad50 Protein at Physiological pH

In nature, thiolate-based systems are the primary targets of divalent mercury (Hg^II ) toxicity. The formation of Hg(Cys)_x cores in catalytic and structural protein centers mediates mercury's toxic effects and ultimately leads to cellular damage. Multiple studies have revealed distinct Hg^II -thiolate coordination preferences, among which linear Hg^II complexes are the most commonly observed in solution at physiological pH. Trigonal or tetrahedral geometries are formed at basic pH or in tight intraprotein Cys-rich metal sites. So far, no interprotein tetrahedral Hg^II complex formed at neutral pH has been reported. Rad50 protein is a part of the multiprotein MRN complex, a major player in DNA damage-repair processes. Its central region consists of a conserved CXXC motif that enables dimerization of two Rad50 molecules by coordinating Zn^II . Dimerized motifs form a unique interprotein zinc hook domain (Hk) that is critical for the biological activity of the MRN. Using a series of length-differentiated peptide models of the Pyrococcus furiosus zinc hook domain, we investigated its interaction with Hg^II . Using UV-Vis, CD, PAC, and ¹⁹⁹ Hg NMR spectroscopies as well as anisotropy decay, we discovered that all Rad50 fragments preferentially form homodimeric Hg(Hk)₂ species with a distorted tetrahedral HgS₄ coordination environment at physiological pH; this is the first example of an interprotein mercury site displaying tetrahedral geometry in solution. At higher Hg^II content, monomeric HgHk complexes with linear geometry are formed. The Hg(Cys)₄ core of Rad50 is extremely stable and does not compete with cyanides, NAC, or DTT. Applying ITC, we found that the stability constant of the Rad50 Hg(Hk)₂ complex is approximately three orders of magnitude higher than those of the strongest Hg^II complexes known to date.

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.

Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance

Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.

Mercury isotope fractionation during methylmercury transport and transformation: A review focusing on analytical method, fractionation characteristics, and its application

Methylmercury (MeHg), a potent neurotoxin, can be formed, migrated and transformed in environmental compartments, accompanying with unique mass-dependent and mass-independent fractionation of mercury (Hg). These Hg isotope fractionation signals have great potential to probe the transformation and transport of MeHg in aquatic environments. However, the majority of studies to date have focused on total Hg isotopic composition, with less attention to the isotopic fractionation of MeHg due to technical difficulties in analysis, which severely hinders the understanding of MeHg isotopic fractionation and its applications. This review a) evaluates the reported analytical methods for Hg isotopic composition of MeHg, including online and offline measurement techniques; b) summarizes the extent and characteristics of Hg isotopic fractionation during MeHg transport and transformation, focusing on methylation, demethylation, trophic transfer and internal metabolism; and c) briefly discusses several applications of MeHg isotopic fractionation signatures in estimating the extent of photodemethylation, tracing the source of Hg species, and diagnosing reaction mechanisms. Additionally, the existing problems and future directions in MeHg isotope fractionation are highlighted to improve the analytical protocol for Hg isotope fractionation and deepen our understanding of Hg isotope fractionation in the biogeochemical cycling of MeHg.

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.