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

Microorganisms Involved in Methylmercury Demethylation and Mercury Reduction are Widely Distributed and Active in the Bathypelagic Deep Ocean Waters

The ocean's mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean is severely data-limited, and the factors controlling MeHg, as well as its transformation rates, remain largely unknown. By analyzing 52 globally distributed bathypelagic deep-ocean metagenomes and 26 new metatranscriptomes from the Malaspina Expedition, our study reveals the widespread distribution and expression of bacterial-coding genes merA and merB in the global bathypelagic ocean (∼4000 m depth). These genes, associated with HgII reduction and MeHg demethylation, respectively, are particularly prevalent within the particle-attached fraction. Moreover, our results indicate that water mass age and the organic matter composition shaped the structure of the communities harboring merA and merB genes living in different particle size fractions, their abundance, and their expression levels. Members of the orders Corynebacteriales, Rhodobacterales, Alteromonadales, Oceanospirillales, Moraxellales, and Flavobacteriales were the main taxonomic players containing merA and merB genes in the deep ocean. These findings, together with our previous results of pure culture isolates of the deep bathypelagic ocean possessing the metabolic capacity to degrade MeHg, indicated that both methylmercury demethylation and HgII reduction likely occur in the global dark ocean, the largest biome in the biosphere.

Dimethylmercury as a Source of Monomethylmercury in a Highly Productive Upwelling System

Monomethylmercury (MMHg) is a neurotoxicant that biomagnifies in marine food webs, reaching high concentrations in apex predators. To predict changes in oceanic MMHg concentrations, it is important to quantify the sources and sinks of MMHg. Here, we study mercury speciation in the California Current System through cruise sampling and modeling. Previous work in the California Current System has found that upwelling transports mercury-enriched deep waters to productive surface waters. These upwelled waters originate within the California Undercurrent water mass and are subsequently advected as a surface water parcel to the California Current. Between the two major water masses, we find that compared to the California Current, the California Undercurrent contains elevated dissolved total mercury (THg) and dimethylmercury (DMHg) concentrations by 59 and 69%, respectively. We explain that these differences result from losses during advection, specifically scavenging of THg and DMHg demethylation. We calculate a net DMHg demethylation rate of 2.0 ± 1.1% d-1 and build an empirically constrained mass budget model to demonstrate that net DMHg demethylation accounts for 61% of surface MMHg sources. These findings illustrate that DMHg is a significant source of MMHg in this region, challenging the current understanding of the major sources of marine MMHg.

Functional genes and microorganisms controlling in situ methylmercury production and degradation in marine sediments: A case study in the Eastern China Coastal Seas

Dominant microorganisms and functional genes, including hgcA, hgcB, merA, and merB, have been identified to be responsible for mercury (Hg) methylation or methylmercury (MeHg) demethylation. However, their in situ correlation with MeHg levels and the processes of Hg methylation and MeHg demethylation in coastal areas remains poorly understood. In this study, four functional genes related to Hg methylation and MeHg demethylation (hgcA, hgcB, merA, and merB) were all detected in the sediments of the Eastern China Coastal Seas (ECCSs) (representative coastal seas highly affected by human activities) using metagenomic approaches. HgcA was identified to be the key gene controlling the in situ net production of MeHg in the ECCSs. Based on metagenomic analysis and incubation experiments, sulfate-reducing bacteria were identified as the dominant microorganisms controlling Hg methylation in the ECCSs. In addition, hgcA gene was positively correlated with the MeHg content and Hg methylation rates, highlighting the potential roles of Hg methylation genes and microorganisms influenced by sediment physicochemical properties in MeHg cycling in the ECCSs. These findings highlighted the necessity of conducting similar studies in other natural systems for elucidating the molecular mechanisms underlying MeHg production in aquatic environments.

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.

Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota

Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.

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.

Thermal stability and micrdose-based coupling CRISPR/Cas12a biosensor for amplification-free detection of hgcA gene in paddy soil

The lack of point-of-use (POU) methods hinders the utilization of the hgcA gene to rapidly evaluate methylmercury risks. CRISPR/Cas12a is a promising technology, but shortcomings such as low sensitivity, a strict reaction temperature and high background signal limit its further utilization. Here, a thermally stable microsystem-based CRISPR/Cas12a biosensor was constructed to achieve POU analysis for hgcA. First, three target gRNAs were designed to recognize hgcA. Then, a microsystem was developed to eliminate the background signal. Next, the effect of temperature on the activity of the Cas12a-gRNA complex was explored and its thermal stability was discovered. After that, coupling gRNA assay was introduced to improve sensitivity, exhibiting a limit of detection as low as 0.49 pM with a linear range of 0.98-125 pM, and a recovery rate between 90 and 110 % for hgcA. The biosensor was finally utilized to assess hgcA abundance in paddy soil, and high abundance of hgcA was found in these paddy soil samples. This study not only systematically explored the influence of temperature and microsystem on CRISPR/Cas12a, providing vital references for other novel CRISPR-based detection methods, but also applied the CRISPR-based analytical method to the field of environmental geochemistry for the first time, demonstrating enormous potential for POU detection in this field.

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.

Interaction of Naturally Occurring Phytoplankton with the Biogeochemical Cycling of Mercury in Aquatic Environments and Its Effects on Global Hg Pollution and Public Health

The biogeochemical cycling of mercury in aquatic environments is a complex process driven by various factors, such as ambient temperature, seasonal variations, methylating bacteria activity, dissolved oxygen levels, and Hg interaction with dissolved organic matter (DOM). As a consequence, part of the Hg contamination from anthropogenic activity that was buried in sediments is reinserted into water columns mainly in highly toxic organic Hg forms (methylmercury, dimethylmercury, etc.). This is especially prominent in the coastal shallow waters of industrial regions worldwide. The main entrance point of these highly toxic Hg forms in the aquatic food web is the naturally occurring phytoplankton. Hg availability, intake, effect on population size, cell toxicity, eventual biotransformation, and intracellular stability in phytoplankton are of the greatest importance for human health, having in mind that such Hg incorporated inside the phytoplankton cells due to biomagnification effects eventually ends up in aquatic wildlife, fish, seafood, and in the human diet. This review summarizes recent findings on the topic of organic Hg form interaction with natural phytoplankton and offers new insight into the matter with possible directions of future research for the prevention of Hg biomagnification in the scope of climate change and global pollution increase scenarios.

Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation

Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21-513 mg kg-1 dry wt. soil; MeHg: 1.21-6.82 ng g-1 dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria.

The Combined Effect of Hg(II) Speciation, Thiol Metabolism, and Cell Physiology on Methylmercury Formation by Geobacter sulfurreducens

The chemical and biological factors controlling microbial formation of methylmercury (MeHg) are widely studied separately, but the combined effects of these factors are largely unknown. We examined how the chemical speciation of divalent, inorganic mercury (Hg(II)), as controlled by low-molecular-mass thiols, and cell physiology govern MeHg formation by Geobacter sulfurreducens. We compared MeHg formation with and without addition of exogenous cysteine (Cys) to experimental assays with varying nutrient and bacterial metabolite concentrations. Cysteine additions initially (0-2 h) enhanced MeHg formation by two mechanisms: (i) altering the Hg(II) partitioning from the cellular to the dissolved phase and/or (ii) shifting the chemical speciation of dissolved Hg(II) in favor of the Hg(Cys)₂ complex. Nutrient additions increased MeHg formation by enhancing cell metabolism. These two effects were, however, not additive since cysteine was largely metabolized to penicillamine (PEN) over time at a rate that increased with nutrient addition. These processes shifted the speciation of dissolved Hg(II) from complexes with relatively high availability, Hg(Cys)₂, to complexes with lower availability, Hg(PEN)₂, for methylation. This thiol conversion by the cells thereby contributed to stalled MeHg formation after 2-6 h Hg(II) exposure. Overall, our results showed a complex influence of thiol metabolism on microbial MeHg formation and suggest that the conversion of cysteine to penicillamine may partly suppress MeHg formation in cysteine-rich environments like natural biofilms.

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.

Distribution and phylogeny of mercury methylation, demethylation, and reduction genes in the Seto Inland Sea of Japan

Mercury (Hg) adversely affects human and environmental health. To evaluate the mercury (Hg) speciation (methylation, demethylation, and reduction) of microorganisms in coastal seawater, we analyzed the microbial functional gene sets involved in Hg methylation (hgcA and hgcB), demethylation (merB), and reduction (merA) using a metagenomic approach in the eastern and western parts (the Kii and Bungo channels, respectively) of the Seto Inland Sea (SIS) of Japan. We determined the concentration of dissolved total mercury (dTHg) and methylated mercury (dMeHg) in seawater. The metagenomic analysis detected hgcAB, merA, and merB in both channels, whereas the phylogenies of these genes differed between them. A correlation between Hg concentration (both dTHg and dMeHg) and the relative abundance of each gene was not observed. Our data suggests that microbial Hg methylation and demethylation could occur in the SIS and there could be a distinct microbial Hg speciation process between the Kii and Bungo channels.