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

Global survey of hgcA-carrying genomes in marine and freshwater sediments: Insights into mercury methylation processes

Mercury (Hg) methylation is a microbially mediated process that produces methylmercury (MeHg), a bioaccumulative neurotoxin. A highly conserved gene pair, hgcAB, is required for Hg methylation, which provides a basis for identifying Hg methylators and evaluating their genomic composition. In this study, we conducted a large-scale omics analysis in which 281 metagenomic freshwater and marine sediment samples from 46 geographic locations across the globe were queried. Specific objectives were to examine the prevalence of Hg methylators, to identify horizontal gene transfer (HGT) events involving hgcAB within Hg methylator communities, and to identify associations between hgcAB and microbial biochemical functions/genes. Hg methylators from the phyla Desulfobacterota and Bacteroidota were dominant in both freshwater and marine sediments while Firmicutes and methanogens belonging to Euryarchaeota were identified only in freshwater sediments. Novel Hg methylators were found in the Phycisphaerae and Planctomycetia classes within the phylum Planctomycetota, including potential hgcA-carrying anammox metagenome-assembled genomes (MAGs) from Candidatus Brocadiia. HGT of hgcA and hgcB were identified in both freshwater and marine methylator communities. Spearman's correlation analysis of methylator genomes suggested that in addition to sulfide, thiosulfate, sulfite, and ammonia may be important parameters for Hg methylation processes in sediments. Overall, our results indicated that the biochemical drivers of Hg methylation vary between marine and freshwater sites, lending insight into the influence of environmental perturbances, such as a changing climate, on Hg methylation processes.

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.

Non-mercury methylating microbial taxa are integral to understanding links between mercury methylation and elemental cycles in marine and freshwater sediments

The goal of this study was to explore the role of non-mercury (Hg) methylating taxa in mercury methylation and to identify potential links between elemental cycles and Hg methylation. Statistical approaches were utilized to investigate the microbial community and biochemical functions in relation to methylmercury (MeHg) concentrations in marine and freshwater sediments. Sediments were collected from the methylation zone (top 15 cm) in four Hg-contaminated sites. Both abiotic (e.g., sulfate, sulfide, iron, salinity, total organic matter, etc.) and biotic factors (e.g., hgcA, abundances of methylating and non-methylating taxa) were quantified. Random forest and stepwise regression were performed to assess whether non-methylating taxa were significantly associated with MeHg concentration. Co-occurrence and functional network analyses were constructed to explore associations between taxa by examining microbial community structure, composition, and biochemical functions across sites. Regression analysis showed that approximately 80% of the variability in sediment MeHg concentration was predicted by total mercury concentration, the abundances of Hg methylating taxa, and the abundances of the non-Hg methylating taxa. The co-occurrence networks identified Paludibacteraceae and Syntrophorhabdaceae as keystone non Hg methylating taxa in multiple sites, indicating the potential for syntrophic interactions with Hg methylators. Strong associations were also observed between methanogens and sulfate-reducing bacteria, which were likely symbiotic associations. The functional network results suggested that non-Hg methylating taxa play important roles in sulfur respiration, nitrogen respiration, and the carbon metabolism-related functions methylotrophy, methanotrophy, and chemoheterotrophy. Interestingly, keystone functions varied by site and did not involve carbon- and sulfur-related functions only. Our findings highlight associations between methylating and non-methylating taxa and sulfur, carbon, and nitrogen cycles in sediment methylation zones, with implications for predicting and understanding the impact of climate and land/sea use changes on Hg methylation.

Microbial community function and methylmercury production in oxygen-limited paddy soil

Methylmercury is a neurotoxic compound that can enter rice fields through rainfall or irrigation with contaminated wastewater, and then contaminate the human food chain through the consumption of rice. Flooded paddy soil has a porous structure that facilitates air exchange with the atmosphere, but the presence of trace amounts of oxygen in flooded rice field soil and its impact on microbial-mediated formation of methylmercury is still unclear. We compared the microbial communities and their functions in oxygen-depleted and oxygen-limited paddy soil. We discovered that oxygen-limited paddy soil had higher methylmercury concentration, which was strongly correlated with soil properties and methylation potential. Compared with oxygen-depleted soil, oxygen-limited soil altered the microbial composition based on 16 S rRNA sequences, but not based on hgcA sequences. Moreover, oxygen-limited soil enhanced microbial activity significantly, increasing the abundance of more than half of the KEGG pathways, especially the metabolic pathways that might be involved in methylation. Our study unveils how microbial communities influence methylmercury formation in oxygen-limited paddy soil. ENVIRONMENTAL IMPLICATIONS: This study examined how low oxygen input affects microbial-induced MeHg formation in anaerobic paddy soil. We found that oxygen-limited soil produced more MeHg than oxygen-depleted soil. Oxygen input altered the microbial community structure of 16 S rRNA sequencing in anaerobic paddy soil, but had little impact on the hgcA sequencing community structure. Microbial activity and metabolic functions related to MeHg formation were also higher in oxygen-limited paddy soil. We suggest that oxygen may not be a limiting factor for Hg methylators, and that insufficient oxygen input in flooded paddy soil increases the risk of human exposure to MeHg from rice consumption.

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.

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.

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.

Amendments of nitrogen and sulfur mitigate carbon-promoting effect on microbial mercury methylation in paddy soils

The imbalance of nutrient elements in paddy soil could affect biogeochemical processes; however, how the key elements input influence microbially-driven conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains virtually unknown. Herein, we conducted a series of microcosm experiments to explore the effects of certain species of carbon (C), nitrogen (N) and sulfur (S) on microbial MeHg production in two typical paddy soils (yellow and black soil). Results showed that the addition of C alone into the soils increased MeHg production approximately 2-13 times in the yellow and black soils; while the combined addition of N and C mitigated the C- promoting effect significantly. Added S also had a buffering effect on C-facilitated MeHg production in the yellow soil despite the extent being lower than that of N addition, whereas this effect was not obvious for the black soil. MeHg production was positively correlated with the abundance of Deltaproteobactera-hgcA in both soils, and the changes in MeHg production were related to the shifts of Hg methylating community resulting from C, N, and S imbalance. We further found that the changes in the proportions of dominant Hg methylators such as Geobacter and some unclassified groups could contribute to the variations in MeHg production under different treatments. Moreover, the enhanced microbial syntrophy with adding N and S might contribute to the reduced C-promoting effect on MeHg production. This study has important implications for better understanding of microbes-driven Hg conversion in paddies and wetlands with nutrient elements input.

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.

Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence

Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.

Methylmercury formation in biofilms of Geobacter sulfurreducens

Introduction

Mercury (Hg) is a major environmental pollutant that accumulates in biota predominantly in the form of methylmercury (MeHg). Surface-associated microbial communities (biofilms) represent an important source of MeHg in natural aquatic systems. In this work, we report MeHg formation in biofilms of the iron-reducing bacterium Geobacter sulfurreducens.

Methods

Biofilms were prepared in media with varied nutrient load for 3, 5, or 7 days, and their structural properties were characterized using confocal laser scanning microscopy, cryo-scanning electron microscopy and Fourier-transform infrared spectroscopy.

Results

Biofilms cultivated for 3 days with vitamins in the medium had the highest surface coverage, and they also contained abundant extracellular matrix. Using 3 and 7-days-old biofilms, we demonstrate that G. sulfurreducens biofilms prepared in media with various nutrient load produce MeHg, of which a significant portion is released to the surrounding medium. The Hg methylation rate constant determined in 6-h assays in a low-nutrient assay medium with 3-days-old biofilms was 3.9 ± 2.0 ∙ 10^-14  L ∙ cell^-1 ∙ h^-1, which is three to five times lower than the rates found in assays with planktonic cultures of G. sulfurreducens in this and previous studies. The fraction of MeHg of total Hg within the biofilms was, however, remarkably high (close to 50%), and medium/biofilm partitioning of inorganic Hg (Hg(II)) indicated low accumulation of Hg(II) in biofilms.

Discussion

These findings suggest a high Hg(II) methylation capacity of G. sulfurreducens biofilms and that Hg(II) transfer to the biofilm is the rate-limiting step for MeHg formation in this systems.

Water pollution and environmental policy in artisanal gold mining frontiers: The case of La Toma, Colombia

Artisanal and small-scale gold mining (ASGM) is the largest anthropogenic source of mercury emissions globally. Concern over mercury pollution increases due to its long-term impacts on human health and aquatic and terrestrial ecosystems. Using a participatory research methodology, we gathered social and behavioral information regarding daily practices and water usage by an ASGM community in Suárez, Colombia. Based on this information, we identified 18 sampling sites of water sources commonly used by the community. The samples were analyzed for total mercury, total coliforms, pH, electrical conductivity, and total dissolved oxygen. Physicochemical and microbiological parameters from the water assessment were compared with the drinking water thresholds set by the Colombian regulatory agencies, the EPA, and the WHO. Our results showed that the majority of the samples do not meet one or more quality and safety standards. On average, the sampling sites showed total mercury levels below the regulatory limits; however, the data had considerable variability, and in many cases, individual observations fell above the maximum concentration limit for drinking water. We discuss these results within the larger framework of the regulatory gaps for human and environmental protection in ASGM contexts. The total lack of water, sanitation, and hygiene infrastructure, combined with the long-term consumption of sublethal doses of mercury and other water contaminants, constitutes a significant threat to the well-being of communities and territories that necessitates further research and intervention by institutional authorities.

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.

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.

Four Lentisphaerae Family Metagenome-Assembled Genomes from the South Atlantic Ocean

We present four Lentisphaerae metagenome-assembled genomes (MAGs) from the South Atlantic Ocean. The medium-quality genomes, affiliated with the family of Lentisphaeraceae, ranged from 4.86 to 5.46 Mbp and harbored the genetic capacity to produce secondary metabolites. This resource provides a basis for investigating the functional attributes of this phylum.

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.

Effective and reusable 3D CuxS nanocluster structured magnetic adsorbent for mercury extraction from wastewater

The elimination of mercury from polluted water using an effective, cost-economic, and sustainable method was investigated in this work. A modulated multilayer magnetic Hg²⁺ extractor was prepared with a self-assembly engineering that permitting robust anchoring and uniform distribution of the negatively charged 3D Cu_xS nanocluster onto a polydopamine (PDA) covered positively strengthened Fe₃O₄ surface. The developed PAD@Fe₃O₄ supported copper sulfide composite (Cu_xS/PAD@Fe₃O₄) presented an unparalleled Hg²⁺ uptake performance with adsorption capacity of 1394.61 mg/g (without saturation), and extraordinary selectivity with distribution coefficient value K_d of 17419.2 mL/g. A complexation reaction during Hg²⁺ affinity was taken place on Cu_xS/PAD@Fe₃O₄ surface, and almost no components losses occurring during the adsorption. Furthermore, the as-prepared Cu_xS/PAD@Fe₃O₄ micron-adsorbent can be easily magnetic recovery and recycled with hydrochloric acid elution. The purification of 50 L Hg²⁺ containing wastewater, initial concentration of 20 μg/L can be achieved with Cu_xS/PAD@Fe₃O₄ dosage of 0.1 g and treatment cost of 0.077 US $. The outlet Hg²⁺ concentration met drinking water standard of the United States Environmental Protection Agency. The Cu_xS/PAD@Fe₃O₄ magnetic adsorbent can be fabricated cheaply and holds promise for scale-up applications.

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

Lake snow as a mercury methylation micro-environment in the oxic water column of a deep peri-alpine lake

Hg methylation in the oxic water column of marine environments has been linked to the presence of suspended and settling particles known as marine snow, which acts as a micro-niche for MeHg production. While marine snow has been thoroughly studied, its freshwater counterpart, lake snow, received less attention, even though few works have highlighted its ability to be a micro environment for Hg methylation in freshwater systems. Here we present new data of MeHg and THg concentrations in the lake snow of a deep peri-alpine lake (Lake Geneva, Switzerland-France). Particles were sampled from the lake and from its main tributaries using continuous flow filtration and continuous flow centrifugation, respectively. MeHg concentrations ranged from 0.48 ± 0.09 ng/g to 9.61 ± 0.67 ng/g in the lake particles, and from 0.30 ± 0.08 ng/g to 2.41 ± 0.14 ng/g in tributary particles. Our results suggest that lake snow is a likely micro-niche for Hg methylation, like marine snow, and that this methylation takes place inside the particles with a subsequent diffusion to the water column. Moreover, we propose a conceptual model to explain the MeHg behavior related to the lake snow along Lake Geneva water column and a mass balance model to estimate the time required to reach the steady state of MeHg in the water column. Our calculation indicates that the steady-state is reached after 37 days. This result is compatible with particles residence times from the literature on Lake Geneva. These particles forming the lake snow are probably a major entry point into the lake's food chain.

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.

Removal of methylmercury and its potential relationship to microbiota in sludge anaerobic digestion under thermal hydrolysis

Reducing health risk of mercury (Hg)/methylmercury (MeHg) in sewage sludge is vital to its land application. This study revealed that thermal hydrolysis reduced MeHg content both during pretreatment process and subsequent anaerobic digestion (AD), which resulted in decrease of MeHg content from 4.24 ng/g to 0.95 ng/g after thermal hydrolysis (150 ℃) and further decreased to 0.39 ng/g after AD. Notably, thermal hydrolysis at high temperature (120 ℃ and 150 ℃) promoted both Hg methylation and MeHg demethylation rather than the control or at low temperature (100 ℃). Hg methylation dominated in hydrolysis and acidogenesis stage, whereas MeHg demethylation dominated in methanogenesis stage. Though abundance of related genes (HgcA and merA) was dramatically reduced, Ruminococcaceae, Peptococcaceae, and Lachnospiraceae were potentially Hg methylators in hydrolysis and acidogenesis stage. Whereas, MeHg demethylation dominated in the late period of AD due to the improved syntrophic methanogenesis and possibly reduced Hg²⁺ biodegradability by precipitation.

Nutrient Inputs Stimulate Mercury Methylation by Syntrophs in a Subarctic Peatland

Climate change dramatically impacts Arctic and subarctic regions, inducing shifts in wetland nutrient regimes as a consequence of thawing permafrost. Altered hydrological regimes may drive changes in the dynamics of microbial mercury (Hg) methylation and bioavailability. Important knowledge gaps remain on the contribution of specific microbial groups to methylmercury (MeHg) production in wetlands of various trophic status. Here, we measured aqueous chemistry, potential methylation rates (k_meth), volatile fatty acid (VFA) dynamics in peat-soil incubations, and genetic potential for Hg methylation across a groundwater-driven nutrient gradient in an interior Alaskan fen. We tested the hypotheses that (1) nutrient inputs will result in increased methylation potentials, and (2) syntrophic interactions contribute to methylation in subarctic wetlands. We observed that concentrations of nutrients, total Hg, and MeHg, abundance of hgcA genes, and rates of methylation in peat incubations (k_meth) were highest near the groundwater input and declined downgradient. hgcA sequences near the input were closely related to those from sulfate-reducing bacteria (SRB), methanogens, and syntrophs. Hg methylation in peat incubations collected near the input source (FPF2) were impacted by the addition of sulfate and some metabolic inhibitors while those down-gradient (FPF5) were not. Sulfate amendment to FPF2 incubations had higher k_meth relative to unamended controls despite no effect on k_meth from addition of the sulfate reduction inhibitor molybdate. The addition of the methanogenic inhibitor BES (25 mM) led to the accumulation of VFAs, but unlike molybdate, it did not affect Hg methylation rates. Rather, the concurrent additions of BES and molybdate significantly decreased k_meth, suggesting a role for interactions between SRB and methanogens in Hg methylation. The reduction in k_meth with combined addition of BES and molybdate, and accumulation of VFA in peat incubations containing BES, and a high abundance of syntroph-related hgcA sequences in peat metagenomes provide evidence for MeHg production by microorganisms growing in syntrophy. Collectively the results suggest that wetland nutrient regimes influence the activity of Hg methylating microorganisms and, consequently, Hg methylation rates. Our results provide key information about microbial Hg methylation and methylating communities under nutrient conditions that are expected to become more common as permafrost soils thaw.

Enhanced Susceptibility of Methylmercury Bioaccumulation into Seston of the Laurentian Great Lakes

Mercury concentrations in the Laurentian Great Lakes waters are among the lowest reported in the literature, while game fish concentrations approach consumption advisory limits, particularly in Lakes Superior, Huron, and Michigan, indicating efficient methylmercury transfer from water to game fish. To determine if increased transfer efficiency is evident within the lower food web, we measured (2010-2018) mercury and dissolved organic carbon (DOC) in water, and in size-sieved seston, dietary tracers (carbon and nitrogen isotope ratios), phytoplankton methylmercury bioaccumulation, and methylmercury biomagnification between increasing seston size fractions. We observed consistently low filter-passing methylmercury (<0.010 ng L-1) and comparatively variable DOC (1.1 to 3.4 mg L-1) concentrations. Methylmercury biomagnification factors between size-sieved seston were similar between lakes. Bioaccumulation factors in phytoplankton were among the highest in the literature (log 5.5 to 6.1), exceeding those in oceans, smaller lakes, and streams, and was influenced by DOC. Higher bioaccumulation rates increase the susceptibility of methylmercury accumulation into the food web. Because mercury is dominantly delivered to the Great Lakes through the atmosphere and the biota therein is highly susceptible to methylmercury uptake, we propose that the Laurentian Great Lakes are excellent sentinels to trace the success of efforts to decrease global mercury emissions (e.g., Minamata Treaty) in the future.

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennessee (United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.

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.