Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes

A comprehensive sulfate and DOM framework to assess methylmercury formation and risk in subtropical wetlands

Wetlands play a vital role in contaminant cycling and uptake. Understanding how sulfate (SO42‒) influences the conversion of inorganic mercury (Hg(II)) to toxic methylmercury (MeHg) is critical for predicting wetland responses to land use and climate change. Here, we sampled surface and pore waters across SO42‒ gradients in three freshwater Everglades wetlands to assess linkages between SO42‒, MeHg, dissolved organic matter (DOM), and inorganic sulfide (S(‒II)). Increasing SO42‒ concentrations increase S(‒II) and DOM concentrations and DOM aromaticity. MeHg concentration show a unimodal response to surface water SO42‒, which reflect high Hg(II) methylation at low-to-intermediate SO42‒concentration (2-12 mg/L) and low Hg(II) methylation at higher SO42‒concentrations ( > 12 mg/L). MeHg concentrations in surface waters correlate positively with MeHg concentrations in prey fish. The coherent biogeochemical relationships between SO42‒ and MeHg concentrations and biologic uptake improve MeHg risk assessment for aquatic food webs and are globally relevant due to anthropogenic and climate-driven increases in SO42‒.

Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment

Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g-1 dw d-1). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.

Sulfate Reduction Drives Elevated Methylmercury Formation in the Water Column of a Eutrophic Freshwater Lake

Mercury (Hg) contamination of aquatic food webs is controlled in part by the formation and accumulation of toxic and bioaccumulative methylmercury (MeHg). MeHg production is mediated by metabolically diverse microorganisms carrying the hgcAB gene pair, while the demethylation reaction is mediated by several biotic and abiotic processes. However, the relative importance of these two processes on MeHg accumulation and the environmental factors that influence them are poorly characterized, especially in eutrophic environments. In this study, both Hg methylation and MeHg demethylation in a eutrophic freshwater lake were linked to ambient MeHg concentrations and hgcA abundance and expression. High methylation rate potentials indicated in situ MeHg formation was a key source of MeHg to the water column, driven by high hgcA abundance and transcription. Molybdate treatment decreased methylation rate potentials, highlighting the importance of sulfate reduction in driving MeHg formation. Sulfate-reducing bacteria accounted for over 50% of the hgcA gene transcription, despite representing less than 10% of the hgcA-carrying microbial community. An arsR-like transcriptional regulator preceded many hgcA sequences; these were transcriptionally active and linked to lower hgcA expression. Overall, this study elucidates the microbial and biogeochemical processes that influence the in situ formation of MeHg in understudied eutrophic freshwater environments.

Total mercury and methylmercury in lake water in years before and after removal of mercury-polluted pulp fiber sediment

There is an elevated presence of mercury (Hg) in the biosphere because of anthropogenic activities. The resulting damage to ecosystems and human health increases dramatically when microorganisms produce highly toxic methylmercury (MeHg). Total Hg (THg), MeHg and ancillary water chemistry were measured in two connected lakes, separated by a short stream stretch, before (1996, 1998 and 2003) and after (2007, 2009 and 2010) the removal of Hg-polluted pulp fiber sediment. Over the study period, there was a decrease in sulfate in the surface water of both lakes, presumably because of declining atmospheric sulfate deposition. Together, the reductions in OM, sulfate, and Hg, resulted in decreased MeHg concentrations as well as decreased MeHg:THg ratios in the bottom water overlying the sediment. There was also a reduction in zooplankton MeHg and fish total Hg in both lakes. Multiple regressions, using the bottom water data before and after remediation from both lakes, indicated that both the yearly maximum MeHg concentration [MeHgmax] and MeHgmax:THg correlated positively with the simultaneously measured sulfate deficit (a proxy for microbial sulfate reduction) and inorganic Hg concentration (IHg = THg - MeHg). This may suggest that the removal of Hg and the decreased sulfate reduction not only led to a decrease in available Hg substrate for methylation but also disfavored the Hg methylation process. As opposed to sulfate deficit, other measurements reflecting heterotrophic microbial activity such as inorganic carbon (IC), ammonium (NH4+), and iron (Fe) did not show significant correlations with MeHg or MeHg:THg when the data from both lakes were combined.

The origin of methyl group in methanogen-mediated mercury methylation: From the Wolfe cycle

Methylmercury (MeHg) is a bioaccumulating neurotoxin mainly produced by anaerobic microorganisms, with methanogen being one of the important methylators. A critical aspect for understanding the mechanism for microbial mercury (Hg) methylation is the origin of the methyl group. However, the origin of methyl group in methanogen-mediated Hg methylation remains unclear. This study aims to identify the source of methyl group for MeHg synthesis in methanogens. Our study revealed that Hg methylation in Methanospirillum hungatei JF-1 is closely related to methanogenesis process, according to the results of proteomic study and substrate limitation study. Next, we proved that nearly all methyl group in MeHg derives from the Wolfe cycle in this species, rather than the previously demonstrated acetyl-coenzyme A pathway, based on the results of 13C labeling study. We then proposed the Wolfe cycle-dependent Hg methylation mechanism in this species. Further genome analyses and 13C labeling experiments indicated that the involvement of the Wolfe cycle in Hg methylation is probably a universal feature among Hg-methylating methanogens. These findings reveal a unique Hg methylation mechanism in methanogens. Our study broadens the carbon substrates and controlling factors for MeHg synthesis in the environment, which can inform the prediction of MeHg production potential and remediation strategies for MeHg contamination.

The different effects of molybdate on Hg(II) bio-methylation in aerobic and anaerobic bacteria

In nature, methylmercury (MeHg) is primarily generated through microbial metabolism, and the ability of bacteria to methylate Hg(II) depends on both bacterial properties and environmental factors. It is widely known that, as a metabolic analog, molybdate can inhibit the sulfate reduction process and affect the growth and methylation of sulfate-reducing bacteria (SRB). However, after it enters the cell, molybdate can be involved in various intracellular metabolic pathways as a molybdenum cofactor; whether fluctuations in its concentration affect the growth and methylation of aerobic mercury methylating strains remains unknown. To address this gap, aerobic γ-Proteobacteria strains Raoultella terrigena TGRB3 (B3) and Pseudomonas putida TGRB4 (B4), as well as an obligate anaerobic δ-Proteobacteria strain of the SRB Desulfomicrobium escambiense CGMCC 1.3481 (DE), were used as experimental strains. The growth and methylation ability of each strain were analyzed under conditions of 500 ng·L-1 Hg(II), 0 and 21% of oxygen, and 0, 0.25, 0.50, and 1 mM of MoO4 2-. In addition, in order to explore the metabolic specificity of aerobic strains, transcriptomic data of the facultative mercury-methylated strain B3 were further analyzed in an aerobic mercuric environment. The results indicated that: (a) molybdate significantly inhibited the growth of DE, while B3 and B4 exhibited normal growth. (b) Under anaerobic conditions, in DE, the MeHg content decreased significantly with increasing molybdate concentration, while in B3, MeHg production was unaffected. Furthermore, under aerobic conditions, the MeHg productions of B3 and B4 were not influenced by the molybdate concentration. (c) The transcriptomic analysis showed several genes that were annotated as members of the molybdenum oxidoreductase family of B3 and that exhibited significant differential expression. These findings suggest that the differential expression of molybdenum-binding proteins might be related to their involvement in energy metabolism pathways that utilize nitrate and dimethyl sulfoxide as electron acceptors. Aerobic bacteria, such as B3 and B4, might possess distinct Hg(II) biotransformation pathways from anaerobic SRB, rendering their growth and biomethylation abilities unaffected by molybdate.

Functional Genes and Transcripts Indicate the Existent and Active Microbial Mercury-Methylating Community in Mangrove Intertidal Sediments of an Urbanized Bay

Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely investigated. An effort to assess the diversity and abundance of hgcA genes and transcripts and link them to Hg and MeHg contents was made in the mangrove intertidal sediments along the urbanized Shenzhen Bay, China. The hgcA genes and transcripts associated with Thermodesulfobacteria [mainly Geobacteraceae, Syntrophorhabdaceae, Desulfobacterales, and Desulfarculales (these four lineages were previously classified into the Deltaproteobacteria taxon)], as well as Euryarchaeota (mainly Methanomicrobia and Theionarchaea) dominated the hgcA-harboring communities, while Chloroflexota, Nitrospirota, Planctomycetota, and Lentisphaerota-like hgcA sequences accounted for a small proportion. The hgcA genes appeared in greater abundance and diversity than their transcript counterparts in each sampling site. Correlation analysis demonstrated that the MeHg content rather than Hg content significantly correlated with the structure of the existent/active hgcA-harboring community and the abundance of hgcA genes/transcripts. These findings provide better insights into the microbial Hg methylation drivers in mangrove sediments, which could be helpful for understanding the MeHg biotransformation therein.

A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances

Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.

Soil Geobacteraceae are the key predictors of neurotoxic methylmercury bioaccumulation in rice

Contamination of rice by the potent neurotoxin methylmercury (MeHg) originates from microbe-mediated Hg methylation in soils. However, the high diversity of Hg methylating microorganisms in soils hinders the prediction of MeHg formation and challenges the mitigation of MeHg bioaccumulation via regulating soil microbiomes. Here we explored the roles of various cropland microbial communities in MeHg formation in the potentials leading to MeHg accumulation in rice and reveal that Geobacteraceae are the key predictors of MeHg bioaccumulation in paddy soil systems. We characterized Hg methylating microorganisms from 67 cropland ecosystems across 3,600 latitudinal kilometres. The simulations of a rice-paddy biogeochemical model show that MeHg accumulation in rice is 1.3-1.7-fold more sensitive to changes in the relative abundance of Geobacteraceae compared to Hg input, which is recognized as the primary parameter in controlling MeHg exposure. These findings open up a window to predict MeHg formation and accumulation in human food webs, enabling more efficient mitigation of risks to human health through regulations of key soil microbiomes.

Recent advance of microbial mercury methylation in the environment

Methylmercury formation is mainly driven by microbial-mediated process. The mechanism of microbial mercury methylation has become a crucial research topic for understanding methylation in the environment. Pioneering studies of microbial mercury methylation are focusing on functional strain isolation, microbial community composition characterization, and mechanism elucidation in various environments. Therefore, the functional genes of microbial mercury methylation, global isolations of Hg methylation strains, and their methylation potential were systematically analyzed, and methylators in typical environments were extensively reviewed. The main drivers (key physicochemical factors and microbiota) of microbial mercury methylation were summarized and discussed. Though significant progress on the mechanism of the Hg microbial methylation has been explored in recent decade, it is still limited in several aspects, including (1) molecular biology techniques for identifying methylators; (2) characterization methods for mercury methylation potential; and (3) complex environmental properties (environmental factors, complex communities, etc.). Accordingly, strategies for studying the Hg microbial methylation mechanism were proposed. These strategies include the following: (1) the development of new molecular biology methods to characterize methylation potential; (2) treating the environment as a micro-ecosystem and studying them from a holistic perspective to clearly understand mercury methylation; (3) a more reasonable and sensitive inhibition test needs to be considered. KEY POINTS: • Global Hg microbial methylation is phylogenetically and functionally discussed. • The main drivers of microbial methylation are compared in various condition. • Future study of Hg microbial methylation is proposed.

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016-2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

Bravo A, Heimburger Boavida LE. Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea

In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.

Consortia cultivation of the Desulfobacterota from macrophyte periphyton: tool for increasing the cultivation of microorganisms involved in mercury methylation

Invasive macrophytes are a persistent environmental problem in aquatic ecosystems. They also cause potential health issues, since periphyton colonizing their aquatic roots are hot spot of mercury methylation. Because periphytons are at the base of the trophic chain, the produced methylmercury is bioamplified through the food webs. In this work, a consortia cultivation approach was applied in order to investigate methylators in the periphyton of Ludwigia sp., an invasive macrophyte. Five growth conditions were used in order to favor the growth of different sulfate reducers, the major mercury methylators in this periphyton. A total of 33 consortia containing putative Hg methylators were obtained. Based on the amino acid sequences of HgcA (essential enzyme for Hg methylation), the obtained consortia could be subdivided into five main clusters, affiliated with Desulfovibrionaceae, Desulfobulbaceae and Syntrophobacteraceae. The main cluster, related to Desulfovibrionaceae, showed the highest sequence diversity; notwithstanding most of the sequences of this cluster showed no close representatives. Through the consortia approach, species thus far uncultivated were cultivated. The successful cultivation of these species was probably possible through the metabolites produced by other members of the consortium. The analysis of the microbial composition of the consortia uncover certain microbial interactions that may exist within this complex environment.

MeHg production in eutrophic lakes: Focusing on the roles of algal organic matter and iron-sulfur-phosphorus dynamics

The mechanisms by which eutrophication affects methylmercury (MeHg) production have not been comprehensively summarized, which hinders accurately predicting the MeHg risk in eutrophic lakes. In this review, we first discussed the effects of eutrophication on biogeochemical cycle of mercury (Hg). Special attentions were paid to the roles of algal organic matter (AOM) and iron (Fe)-sulfur (S)-phosphorus (P) dynamics in MeHg production. Finally, the suggestions for risk control of MeHg in eutrophic lakes were proposed. AOM can affect in situ Hg methylation by stimulating the abundance and activities of Hg methylating microorganisms and regulating Hg bioavailability, which are dependent on bacteria-strain and algae species, the molecular weight and composition of AOM as well as environmental conditions (e.g., light). Fe-S-P dynamics under eutrophication including sulfate reduction, FeS formation and P release could also play crucial but complicated roles in MeHg production, in which AOM may participate through influencing the dissolution and aggregation processes, structural order and surface properties of HgS nanoparticles (HgS_NP). Future studies should pay more attention to the dynamics of AOM in responses to the changing environmental conditions (e.g., light penetration and redox fluctuations) and how such variations will subsequently affect MeHg production. The effects of Fe-S-P dynamics on MeHg production under eutrophication also deserve further investigations, especially the interactions between AOM and HgS_NP. Remediation strategies with lower disturbance, greater stability and less cost like the technology of interfacial O₂ nanobubbles are urgent to be explored. This review will deepen our understanding of the mechanisms of MeHg production in eutrophic lakes and provide theoretical guidance for its risk control.

Global change effects on biogeochemical mercury cycling

Past and present anthropogenic mercury (Hg) release to ecosystems causes neurotoxicity and cardiovascular disease in humans with an estimated economic cost of $117 billion USD annually. Humans are primarily exposed to Hg via the consumption of contaminated freshwater and marine fish. The UNEP Minamata Convention on Hg aims to curb Hg release to the environment and is accompanied by global Hg monitoring efforts to track its success. The biogeochemical Hg cycle is a complex cascade of release, dispersal, transformation and bio-uptake processes that link Hg sources to Hg exposure. Global change interacts with the Hg cycle by impacting the physical, biogeochemical and ecological factors that control these processes. In this review we examine how global change such as biome shifts, deforestation, permafrost thaw or ocean stratification will alter Hg cycling and exposure. Based on past declines in Hg release and environmental levels, we expect that future policy impacts should be distinguishable from global change effects at the regional and global scales.

Biogeochemical and hydrologic synergy control mercury fate in an arid land river-reservoir system

Reservoirs in arid landscapes provide critical water storage and hydroelectric power but influence the transport and biogeochemical cycling of mercury (Hg). Improved management of reservoirs to mitigate the supply and uptake of bioavailable methylmercury (MeHg) in aquatic food webs will benefit from a mechanistic understanding of inorganic divalent Hg (Hg(II)) and MeHg fate within and downstream of reservoirs. Here, we quantified Hg(II), MeHg, and other pertinent biogeochemical constituents in water (filtered and associated with particles) at high temporal resolution from 2016-2020. This was done (1) at inflow and outflow locations of three successive hydroelectric reservoirs (Snake River, Idaho, Oregon) and (2) vertically and longitudinally within the first reservoir (Brownlee Reservoir). Under spring high flow, upstream inputs of particulate Hg (Hg(II) and MeHg) and filter-passing Hg(II) to Brownlee Reservoir were governed by total suspended solids and dissolved organic matter, respectively. Under redox stratified conditions in summer, net MeHg formation in the meta- and hypolimnion of Brownlee reservoir yielded elevated filter-passing and particulate MeHg concentrations, the latter exceeding 500 ng g^-1 on particles. Simultaneously, the organic matter content of particulates increased longitudinally in the reservoir (from 9-29%) and temporally with stratified duration. In late summer and fall, destratification mobilized MeHg from the upgradient metalimnion and the downgradient hypolimnion of Brownlee Reservoir, respectively, resulting in downstream export of elevated filter-passing MeHg and organic-rich particles enriched in MeHg (up to 43% MeHg). We document coupled biogeochemical and hydrologic processes that yield in-reservoir MeHg accumulation and MeHg export in water and particles, which impacts MeHg uptake in aquatic food webs within and downstream of reservoirs.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Mercury in wetlands over 60 years: Research progress and emerging trends

Wetlands are considered the hotspots for mercury (Hg) biogeochemistry, garnering global attention. Therefore, it is important to review the research progress in this field and predict future frontiers. To achieve that, we conducted a literature analysis by collecting 15,813 publications about Hg in wetlands from the Web of Science Core Collection. The focus of wetland Hg research has changed dramatically over time: 1) In the initial stage (i.e., 1959-1990), research mainly focused on investigating the sources and contents of Hg in wetland environments and fish. 2) For the next 20 years (i.e., 1991-2010), Hg transformation (e.g., Hg reduction and methylation) and environmental factors that affect Hg bioaccumulation have attracted extensive attention. 3) In the recent years of 2011-2022, hot topics in Hg study include microbial Hg methylators, Hg bioavailability, methylmercury (MeHg) demethylation, Hg stable isotope, and Hg cycling in paddy fields. Finally, we put forward future research priorities, i.e., 1) clarifying the primary factors controlling MeHg production, 2) uncovering the MeHg demethylation process, 3) elucidating MeHg bioaccumulation process to better predict its risk, and 4) recognizing the role of wetlands in Hg circulation. This research shows a comprehensive knowledge map for wetland Hg research and suggests avenues for future studies.

Potential for mercury methylation by Asgard archaea in mangrove sediments

Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.

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.

Anaerobic mercury methylators inhabit sinking particles of oxic water columns

Increased concentration of mercury, particularly methylmercury, in the environment is a worldwide concern because of its toxicity in severely exposed humans. Although the formation of methylmercury in oxic water columns has been previously suggested, there is no evidence of the presence of microorganisms able to perform this process, using the hgcAB gene pair (hgc⁺ microorganisms), in such environments. Here we show the prevalence of hgc⁺ microorganisms in sinking particles of the oxic water column of Lake Geneva (Switzerland and France) and its anoxic bottom sediments. Compared to anoxic sediments, sinking particles found in oxic waters exhibited relatively high proportion of hgc⁺genes taxonomically assigned to Firmicutes. In contrast hgc⁺members from Nitrospirae, Chloroflexota and PVC superphylum were prevalent in anoxic sediment while hgc⁺ Desulfobacterota were found in both environments. Altogether, the description of the diversity of putative mercury methylators in the oxic water column expand our understanding on MeHg formation in aquatic environments and at a global scale.

Impacts of the invasive Spartina anglica on C-S-Hg cycles and Hg(II) methylating microbial communities revealed by hgcA gene analysis in intertidal sediment of the Han River estuary, Yellow Sea

We investigated the impact of invasive vegetation on mercury cycles, and identified microorganisms directly related to Hg(II) methylation using hgcA gene in vegetated mud flats (VMF) inhabited by native Suaeda japonica (SJ) and invasive Spartina anglica (SA), and unvegetated mud flats (UMF) in Ganghwa intertidal sediments. Sulfate reduction rate (SRR) and rate constants of Hg(II) methylation (K_m) and methyl-Hg demethylation (K_d) were consistently greater in VMF than in UMF, specifically 1.5, 2 and 11.7 times higher, respectively, for SA. Both K_m and K_d were significantly correlated with SRR and the abundance of sulfate-reducing bacteria. These results indicate that the rhizosphere of invasive SA provides a hotspot for Hg dynamics coupled with sulfate reduction. HgcA gene analysis revealed that Hg(II)-methylators were dominated by Deltaproteobacteria, Chloroflexi and Euryarchaeota, comprising 37.9%, 35.8%, and 6.5% of total hgcA gene sequences, respectively, which implies that coastal sediments harbor diverse Hg(II)-methylating microorganisms that previously underrepresented.

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.

Understanding of mercury and methylmercury transformation in sludge composting by metagenomic analysis

Municipal sewage especially the produced sewage sludge is a significant source releasing mercury (Hg) to the environment. However, the Hg speciation especially methylmercury (MeHg) transformation in sewage sludge treatment process remains poorly understood. This study investigated the transformation of Hg speciation especially MeHg in sludge composting. The distribution of Hg transformation related gene pairs hgcAB and merAB, and their putative microbial hosts were comprehensively analyzed. Both Hg (from 3.16±0.22 mg/kg to 3.20±0.19 mg/kg) and MeHg content (from 4.77±0.64 ng/g to 4.36±0.37 ng/g) were not obviously changed before and after composting, but about 19.69% of Hg and 27.36% of MeHg were lost according to mass balance calculation. The metagenomic analysis further revealed that anaerobes (Desulfobacterota and Euryarchaeota) were the mainly putative Hg methylators especially carrying high abundance of hgcA gene in the initial periods of composting. Among the 151 reconstructed metagenome-assembled genomes (MAGs), only 4 hgcA gene carriers (Myxococcota, Firmicutes, Cyclobacteriaceae, and Methanothermobacter) and 16 merB gene carriers were identified. But almost all of the MAGs carried hgcB gene and merA gene. The merA gene was widely distributed in genomes, which indicated the widespread functionality of microbes for reducing Hg(II) to Hg(0). The hgcA carrying microbes tends to present the similar metabolic pathways including methanogenesis and sulfur metabolism. Besides, both the irregular distribution of hgcA in various species (including Actinobacteria, Archaea, Bacteroidetes, Desulfobacterota, Euryarchaeota, and Nitrospirae, etc.) and opposite evolution trends between hgcA gene abundance and its host genome abundance can be an indication of horizontal gene transfer or gene deletions of hgcA during composting. Our findings thus revealed that sludge composting is not only a hotspot for Hg speciation transformation, but also a potential hotspot for MeHg transformation.

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.

Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters

Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (Hg^II) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved Hg^II-sulfide species were strong predictors of both the Hg^II methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc⁺ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc⁺ MAGs), which highlighted the versatility of putative Hg^II methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the Hg^II methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.

Occurrence of methylmercury in aerobic environments: Evidence of mercury bacterial methylation based on simulation experiments

Methylmercury (MeHg) is mainly produced by anaerobic δ-proteobacteria such as sulfate-reducing bacteria (SRB). However, mercury bio-methylation has also been found to occur in the aerobic soil of the Three Gorges Reservoir (TGR). Using γ-proteobacterial TGR bacteria (TGRB) and δ-proteobacterial Desulfomicrobium escambiense strains, the efficiency of mercury methylation and demethylation was evaluated using an isotope tracer technique. Kinetics simulation showed that the bacterial Hg methylation rate (k_m) of TGRB3 was 4.36 × 10^-9 pg·cell^-1·h^-1, which was significantly lower than that of D. escambiense (170.74 ×10^-9 pg·cell^-1·h^-1) under anaerobic conditions. Under facultative and/or aerobic conditions, D. escambiense could not survive, while the k_m of TGRB3 were 0.35 × 10^-9 and 0.29 × 10^-9 pg·cell^-1·h^-1, respectively. Furthermore, the bacterial MeHg tolerance threshold of TGRB3 was 3.47 × 10^-9 pg·cell^-1, which was 98.6-fold lower than that of D. escambiense under anaerobic conditions. However, the MeHg tolerance threshold of TGRB3 remained at 0.50-0.52 × 10^-9 pg·cell^-1 under facultative and/or aerobic conditions. Notably, bacterial Hg methylation rates (k_m) were higher than the corresponding bacterial MeHg demethylation rates (k_d1). These results establish the contribution of some aerobic and/or facultative anaerobic bacteria to net environmental MeHg production in terrestrial ecosystems and provide a novel understanding of the biogeochemical cycle of MeHg. SYNOPSIS: Hg methylation of facultative and/or aerobic bacteria may contribute to the net production of environmental methylmercury in terrestrial ecosystems.

Mercury transformation processes in nature: Critical knowledge gaps and perspectives for moving forward

The transformation of mercury (Hg) in the environment plays a vital role in the cycling of Hg and its risk to the ecosystem and human health. Of particular importance are Hg oxidation/reduction and methylation/demethylation processes driven or mediated by the dynamics of light, microorganisms, and organic carbon, among others. Advances in understanding those Hg transformation processes determine our capacity of projecting and mitigating Hg risk. Here, we provide a critical analysis of major knowledge gaps in our understanding of Hg transformation in nature, with perspectives on approaches moving forward. Our analysis focuses on Hg transformation processes in the environment, as well as emerging methodology in exploring these processes. Future avenues for improving the understanding of Hg transformation processes to protect ecosystem and human health are also explored.

Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments

Laboratory studies used to assess the environmental fate of organic chemicals such as pesticides fail to replicate environmental conditions, resulting in large errors in predicted transformation rates. We combine laboratory and field data to identify the dominant loss processes of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in lakes for the first time. Microbial and photochemical degradation are individually assessed using laboratory-based microcosms and irradiation studies, respectively. Field campaigns are conducted in six lakes to quantify 2,4-D loss following large-scale herbicide treatments. Irradiation studies show that 2,4-D undergoes direct photodegradation, but modeling efforts demonstrated that this process is negligible under environmental conditions. Microcosms constructed using field inocula show that sediment microbial communities are responsible for degradation of 2,4-D in lakes. Attempts to quantify transformation products are unsuccessful in both laboratory and field studies, suggesting that their persistence is not a major concern. The synthesis of laboratory and field experiments is used to demonstrate best practices in designing laboratory persistence studies and in using those results to mechanistically predict contaminant fate in complex aquatic environments.

Microbial mercury transformations: Molecules, functions and organisms

Mercury (Hg) methylation, methylmercury (MeHg) demethylation, and inorganic redox transformations of Hg are microbe-mediating processes that determine the fate and cycling of Hg and MeHg in many environments, and by doing so influence the health of humans and wild life. The discovery of the Hg methylation genes, hgcAB, in the last decade together with advances in high throughput and genome sequencing methods, have resulted in an expanded appreciation of the diversity of Hg methylating microbes. This review aims to describe experimentally confirmed and recently discovered hgcAB gene-carrying Hg methylating microbes; phylogenetic and taxonomic analyses are presented. In addition, the current knowledge on transformation mechanisms, the organisms that carry them out, and the impact of environmental parameters on Hg methylation, MeHg demethylation, and inorganic Hg reduction and oxidation is summarized. This knowledge provides a foundation for future action toward mitigating the impact of environmental Hg pollution.

Nitrospina-like Bacteria Are Dominant Potential Mercury Methylators in Both the Oyashio and Kuroshio Regions of the Western North Pacific

Highly neurotoxic methylmercury (MeHg) accumulates in marine organisms, thereby negatively affecting human and environmental health. Recent studies have revealed that oceanic prokaryotes harboring the hgcAB gene pair are involved in Hg methylation. Presently, little is known about the distribution and phylogeny of these genes in distinct oceanic regions of the western North Pacific. In this study, we used metagenomics to survey the distribution of hgcAB genes in the seawater columns of the subarctic Oyashio region and the subtropical Kuroshio region. The hgcAB genes were detected in the MeHg-rich offshore mesopelagic layers of both the Oyashio region, which is a highly productive area in the western North Pacific, and the Kuroshio region, which has low productivity. Comparative analysis revealed that hgcAB genes belonging to the Nitrospina-like lineage were dominant in the MeHg-rich mesopelagic layers of both regions. These results indicate that Nitrospina-like bacteria are the dominant Hg methylators in the mesopelagic layers throughout the western North Pacific. IMPORTANCE MeHg is highly neurotoxic and accumulates in marine organisms. Thus, understanding MeHg production in seawater is critical for environmental and human health. Recent studies have shown that microorganisms harboring mercury-methylating genes (hgcA and hgcB) are involved in MeHg production in several marine environments. Knowing the distribution and phylogeny of hgcAB genes in seawater columns can facilitate assessment of microbial MeHg production in the ocean. We report that hgcAB genes affiliated with the microaerophilic Nitrospina lineage were detected in the MeHg-rich mesopelagic layers of two hydrologically distinct oceanic regions of the western North Pacific. This finding facilitates understanding of the microbial Hg methylation and accumulation in seawater columns of the western North Pacific.

Coupling oxidation of acid volatile sulfide, ferrous iron, and ammonia nitrogen from black-odorous sediment via autotrophic denitrification-anammox by nitrate addition

The coupling removal of acid volatile sulfide (AVS), ferrous iron, and ammonia nitrogen has been applied for black-odorous sediment remediation. In this study, calcium nitrate with different N/(S + Fe) ratios (0.45, 0.90, 1.20 and 1.80) was added into black-odorous sediment in four systems named R1, R2, R3, and R4. Results showed that the removal rate of AVS was 76.40% in the R1, which was lower compared with rates in R2-R4 around 96.70%. The ferrous oxidation rate was approximately 87.00% in R2-R4, which was considerably higher than that in the R1 (24.62%). And the ammonia was reduced by 81.02%, 88.00%, 100%, and 57.18% in R1, R2, R3 and R4, respectively. During the reaction, nitrite accumulation was observed, indicating partial denitrification. Moreover, microbes related to autotrophic denitrification (e.g., genus Thiobacillus, Dok59, GOUTA19, Gallionella, with the highest abundance of 15.40%, 13.21%, 8.79%, 9.44%, respectively) were detected in all systems. Furthermore, the anammox bacteria Candidatus_Brocadia with the highest abundance of 3.44% and 4.00% in R2 and R3, respectively was also found. These findings confirmed that AVS, ferrous iron, and ammonia nitrogen could be simultaneously removed via autotrophic denitrification coupled with anammox in black-odorous sediment by nitrate addition.

Role of organic matter and microbial communities in mercury retention and methylation in sediments near run-of-river hydroelectric dams

Run-of-river power plants (RoRs) are expected to triple in number over the next decades in Canada. These structures are not anticipated to considerably promote the mobilization and transport of mercury (Hg) and its subsequent microbial transformation to methylmercury (MeHg), a neurotoxin able to biomagnify in food webs up to humans. To test whether construction of RoRs had an effect on Hg transport and transformation, we studied Hg and MeHg concentrations, organic matter contents and methylating microbial community abundance and composition in the sediments of a section of the St. Maurice River (Quebec, Canada). This river section has been affected by the construction of two RoR dams and its watershed has been disturbed by a forest fire, logging, and the construction of wetlands. Higher total Hg (THg) and MeHg concentrations were observed in the surface sediments of the flooded sites upstream of the RoRs. These peaks in THg and MeHg were correlated with organic matter proportions in the sediments (r² = 0.87 and 0.82, respectively). In contrast, the proportion of MeHg, a proxy for methylation potential, was best explained by the carbon to nitrogen ratio suggesting the importance of terrigenous organic matter as labile substrate for Hg methylation in this system. Metagenomic analysis of Hg-methylating communities based on the hgcA functional gene marker indicated an abundance of methanogens, sulfate reducers and fermenters, suggesting that these metabolic guilds may be primary Hg methylators in these surface sediments. We propose that RoR pondages act as traps for sediments, organic matter and Hg, and that this retention can be amplified by other disturbances of the watershed such as forest fire and logging. RoR flooded sites can be conducive to Hg methylation in sediments and may act as gateways for bioaccumulation and biomagnification of MeHg along food webs, particularly in disturbed watersheds.

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands

Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10-3 day-1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day-1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.

Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment

The sulfate-reducing, mercury-methylating strain ND132^T was isolated from the brackish anaerobic bottom sediments of Chesapeake Bay, USA. Capable of high levels of mercury (Hg) methylation, ND132^T has been widely used as a model strain to study the process and to determine the genetic basis of Hg methylation. Originally called Desulfovibrio desulfuricans ND132^T on the basis of an early partial 16S rRNA sequence, the strain has never been formally described. Phylogenetic and physiological traits place this strain within the genus Pseudodesulfovibrio, in the recently reclassified phylum Desulfobacterota (formerly Deltaproteobacteria). ND132^T is most closely related to Pseudodesulfovibrio hydrargyri BerOc1^T and Pseudodesulfovibrio indicus J2^T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1^T and ND132^T, and 84 % similarity between ND132^T and P. indicus J2^T. These cut-off scores <95 %, along with a multi-gene phylogenetic analysis of members of the family Desulfovibrionacea, and differences in physiology indicate that all three strains represent separate species. The Gram-stain-negative cells are vibrio-shaped, motile and not sporulated. ND132^T is a salt-tolerant mesophile with optimal growth in the laboratory at 32 °C, 2 % salinity, and pH 7.8. The DNA G+C content of the genomic DNA is 65.2 %. It is an incomplete oxidizer of short chain fatty acids, using lactate, pyruvate and fumarate with sulfate or sulfite as the terminal electron acceptors. ND132^T can respire fumarate using pyruvate as an electron donor. The major fatty acids are iso-C_15 : 0, anteiso-C_15 : 0, iso-C_17 : 0, iso-C_17 : 1ω9c and anteiso-C_17 : 0. We propose the classification of strain ND132^T (DSM 110689, ATCC TSD-224) as the type strain Pseudodesulfovibrio mercurii sp. nov.

Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake

Mercury (Hg) methylation is a microbially mediated process that converts inorganic Hg into bioaccumulative, neurotoxic methylmercury (MeHg). The metabolic activity of methylating organisms is highly dependent on biogeochemical conditions, which subsequently influences MeHg production. However, our understanding of the ecophysiology of methylators in natural ecosystems is still limited. Here, we identified potential locations of MeHg production in the anoxic, sulfidic hypolimnion of a freshwater lake. At these sites, we used shotgun metagenomics to characterize microorganisms with the Hg-methylation gene hgcA. Putative methylators were dominated by hgcA sequences divergent from those in well-studied, confirmed methylators. Using genome-resolved metagenomics, we identified organisms with hgcA (hgcA+) within the Bacteroidetes and the recently described Kiritimatiellaeota phyla. We identified hgcA+ genomes derived from sulfate-reducing bacteria, but these accounted for only 22% of hgcA+ genome coverage. The most abundant hgcA+ genomes were from fermenters, accounting for over half of the hgcA gene coverage. Many of these organisms also mediate hydrolysis of polysaccharides, likely from cyanobacterial blooms. This work highlights the distribution of the Hg-methylation genes across microbial metabolic guilds and indicate that primary degradation of polysaccharides and fermentation may play an important but unrecognized role in MeHg production in the anoxic hypolimnion of freshwater lakes.

Diverse Communities of hgcAB+ Microorganisms Methylate Mercury in Freshwater Sediments Subjected to Experimental Sulfate Loading

Methylmercury (MeHg) is a bioaccumulative neurotoxin produced by certain sulfate-reducing bacteria and other anaerobic microorganisms. Because microorganisms differ in their capacity to methylate mercury, the abundance and distribution of methylating populations may determine MeHg production in the environment. We compared rates of MeHg production and the distribution of hgcAB genes in epilimnetic sediments from a freshwater lake that were experimentally amended with sulfate levels from 7 to 300 mg L^-1. The most abundant hgcAB sequences were associated with clades of Methanomicrobia, sulfate-reducing Deltaproteobacteria, Spirochaetes, and unknown environmental sequences. The hgcAB⁺ communities from higher sulfate amendments were less diverse and had relatively more Deltaproteobacteria, whereas the communities from lower amendments were more diverse with a larger proportion of hgcAB sequences affiliated with other clades. Potential methylation rate constants varied 52-fold across the experiment. Both potential methylation rate constants and % MeHg were the highest in sediments from the lowest sulfate amendments, which had the most diverse hgcAB⁺ communities and relatively fewer hgcAB genes from clades associated with sulfate reduction. Although pore water sulfide concentration covaried with hgcAB diversity across our experimental sulfate gradient, major changes in the community of hgcAB⁺ organisms occurred prior to a significant buildup of sulfide in pore waters. Our results indicate that methylating communities dominated by diverse anaerobic microorganisms that do not reduce sulfate can produce MeHg as effectively as communities dominated by sulfate-reducing populations.

Relationship Between Hg Speciation and Hg Methylation/Demethylation Processes in the Sulfate-Reducing Bacterium Pseudodesulfovibrio hydrargyri: Evidences From HERFD-XANES and Nano-XRF

Microorganisms are key players in the transformation of mercury into neurotoxic methylmercury (MeHg). Nevertheless, this mechanism and the opposite MeHg demethylation remain poorly understood. Here, we explored the impact of inorganic mercury (IHg) and MeHg concentrations from 0.05 to 50 μM on the production and degradation of MeHg in two sulfate-reducing bacteria, Pseudodesulfovibrio hydrargyri BerOc1 able to methylate and demethylate mercury and Desulfovibrio desulfuricans G200 only able to demethylate MeHg. MeHg produced by BerOc1 increased with increasing IHg concentration with a maximum attained for 5 μM, and suggested a saturation of the process. MeHg was mainly found in the supernatant suggesting its export from the cell. Hg L₃-edge High- Energy-Resolution-Fluorescence-Detected-X-ray-Absorption-Near-Edge-Structure spectroscopy (HERFD-XANES) identified MeHg produced by BerOc1 as MeHg-cysteine₂ form. A dominant tetracoordinated βHgS form was detected for BerOc1 exposed to the lowest IHg concentrations where methylation was detected. In contrast, at the highest exposure (50 μM) where Hg methylation was abolished, Hg species drastically changed suggesting a role of Hg speciation in the production of MeHg. The tetracoordinated βHgS was likely present as nano-particles as suggested by transmission electron microscopy combined to X-ray energy dispersive spectroscopy (TEM-X-EDS) and nano-X ray fluorescence (nano-XRF). When exposed to MeHg, the production of IHg, on the contrary, increased with the increase of MeHg exposure until 50 μM for both BerOc1 and G200 strains, suggesting that demethylation did not require intact biological activity. The formed IHg species were identified as various tetracoordinated Hg-S forms. These results highlight the important role of thiol ligands and Hg coordination in Hg methylation and demethylation processes.

An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature

The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broad-range primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hg-methylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Combined with high-throughput amplicon specific sequencing, the new primer set also indentified novel hgcAB sequences similar to Lentisphaerae, Bacteroidetes, Atribacteria, and candidate phyla WOR-3 and KSB1 bacteria. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature.

Substratum-associated microbiota

Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.

Mercury biogeochemical cycling: A synthesis of recent scientific advances

The focus of this paper is to briefly discuss the major advances in scientific thinking regarding: a) processes governing the fate and transport of mercury in the environment; b) advances in measurement methods; and c) how these advances in knowledge fit in within the context of the Minamata Convention on Mercury. Details regarding the information summarized here can be found in the papers associated with this Virtual Special Issue of STOTEN.

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea

In natural environments, the production of neurotoxic and bioaccumulative methylmercury (MeHg) is mediated by microorganisms carrying the genes hgcA and hgcB. However, the contribution of these microorganisms to mercury (Hg) methylation or MeHg accumulation in the ocean is poorly understood. Here we determined the total Hg (THg) and MeHg concentrations in seawater samples and conducted a metagenomic survey of the hgcAB genes and functional modules involved in metabolic pathways in the East China Sea (ECS). In the metagenomic analyses, we used paired-end reads and assembled contigs for hgcAB enumeration and phylogenetic analyses in the seawater column. To evaluate the relative abundance of hgcAB in the metagenomic data, we estimated the abundance of recA (single-copy gene of bacteria) as well and then compared them. Moreover, the profiles of prokaryotic community composition were analyzed by 16S rRNA gene (V4 region) deep-sequencing. In the mesopelagic layers, the hgcA sequences were detected, and there was a positive correlation between hgcA abundance relative to the recA and MeHg concentrations. Thus, the quantification of the hgcA sequences could provide valuable information to evaluate the potential environments of microbial MeHg accumulation in the seawater column. A phylogenetic analysis using the assembled contigs revealed that all of the hgcA sequences in the mesopelagic layers were affiliated with Nitrospina-like sequences. The 16S rRNA gene analysis revealed that Nitrospinae were abundant in the mesopelagic layers. Although the lineages of Deltaproteobacteria, Firmicutes, and Spirochaetes were detected in the seawater column, their hgcAB sequences were not detected in our metagenomes, despite the fact that they are closely related to previously identified Hg methylators. The metabolic pathway analysis revealed that the modules related to sulfur and methane metabolism were prominent in the mesopelagic layers. However, no hgcA sequences affiliated with sulfate-reducing bacteria (SRB) or methanogens were detected in these layers, suggesting that these bacteria could not be strongly involved in the Hg accumulation in the seawater column. Our results indicate that Nitrospina-like bacteria with hgcAB genes could play a critical role in microbial Hg accumulation in the oxygenated mesopelagic layers of the ECS.

Recent advances in understanding and measurement of mercury in the environment: Terrestrial Hg cycling

This review documents recent advances in terrestrial mercury cycling. Terrestrial mercury (Hg) research has matured in some areas, and is developing rapidly in others. We summarize the state of the science circa 2010 as a starting point, and then present the advances during the last decade in three areas: land use, sulfate deposition, and climate change. The advances are presented in the framework of three Hg "gateways" to the terrestrial environment: inputs from the atmosphere, uptake in food, and runoff with surface water. Among the most notable advances: These and other advances reported here are of value in evaluating the effectiveness of the Minamata Convention on reducing environmental Hg exposure to humans and wildlife.

Biotic formation of methylmercury: A bio-physico-chemical conundrum

Mercury (Hg) is a natural and widespread trace metal, but is considered a priority pollutant, particularly its organic form methylmercury (MMHg), because of human's exposure to MMHg through fish consumption. Pioneering studies showed the methylation of divalent Hg (Hg^II) to MMHg to occur under oxygen-limited conditions and to depend on the activity of anaerobic microorganisms. Recent studies identified the hgcAB gene cluster in microorganisms with the capacity to methylate Hg^II and unveiled a much wider range of species and environmental conditions producing MMHg than previously expected. Here, we review the recent knowledge and approaches used to understand Hg^II-methylation, microbial biodiversity and activity involved in these processes, and we highlight the current limits for predicting MMHg concentrations in the environment. The available data unveil the fact that Hg^II methylation is a bio-physico-chemical conundrum in which the efficiency of biological Hg^II methylation appears to depend chiefly on Hg^II and nutrients availability, the abundance of electron acceptors such as sulfate or iron, the abundance and composition of organic matter as well as the activity and structure of the microbial community. An increased knowledge of the relationship between microbial community composition, physico-chemical conditions, MMHg production, and demethylation is necessary to predict variability in MMHg concentrations across environments.

Understanding mercury methylation in the changing environment: Recent advances in assessing microbial methylators and mercury bioavailability

Methylmercury (MeHg) is a neurotoxin, mainly derived from microbial mercury methylation in natural aquatic environments, and poses threats to human health. Polar regions and paddy soils are potential hotspots of mercury methylation and represent environmental settings that are susceptible to natural and anthropogenic perturbations. The effects of changing environmental conditions on the methylating microorganisms and mercury speciation due to global climate change and farming practices aimed for sustainable agriculture were discussed for polar regions and paddy soils, respectively. To better understand and predict microbial mercury methylation in the changing environment, we synthesized current understanding of how to effectively identify active mercury methylators and assess the bioavailability of different mercury species for methylation. The application of biomarkers based on the hgcAB genes have demonstrated the occurrence of potential mercury methylators, such as sulfate-reducing bacteria, iron-reducing bacteria, methanogen and syntrophs, in a diverse variety of microbial habitats. Advanced techniques, such as enriched stable isotope tracers, whole-cell biosensor and diffusive gradient thin film (DGT) have shown great promises in quantitatively assessing mercury availability to microbial methylators. Improved understanding of the complex structure of microbial communities consisting mercury methylators and non-methylators, chemical speciation of inorganic mercury under geochemically relevant conditions, and the pathway of cellular mercury uptake will undoubtedly facilitate accurate assessment and prediction of in situ microbial mercury methylation.

Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance

Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.