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 (HgII) 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 HgII-sulfide species were strong predictors of both the HgII 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 HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII 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.

Mediterranean Mercury Assessment 2022: An Updated Budget, Health Consequences, and Research Perspectives.

Mercury (Hg) and especially its methylated species (MeHg) are toxic chemicals that contaminate humans via the consumption of seafood. The most recent UNEP Global Mercury Assessment stressed that Mediterranean populations have higher Hg levels than people elsewhere in Europe. The present Critical Review updates current knowledge on the sources, biogeochemical cycling, and mass balance of Hg in the Mediterranean and identifies perspectives for future research especially in the context of global change. Concentrations of Hg in the Western Mediterranean average 0.86 ± 0.27 pmol L-1 in the upper water layer and 1.02 ± 0.12 pmol L-1 in intermediate and deep waters. In the Eastern Mediterranean, Hg measurements are in the same range but are too few to determine any consistent oceanographical pattern. The Mediterranean waters have a high methylation capacity, with MeHg representing up to 86% of the total Hg, and constitute a source of MeHg for the adjacent North Atlantic Ocean. The highest MeHg concentrations are associated with low oxygen water masses, suggesting a microbiological control on Hg methylation, consistent with the identification of hgcA-like genes in Mediterranean waters. MeHg concentrations are twice as high in the waters of the Western Basin compared to the ultra-oligotrophic Eastern Basin waters. This difference appears to be transferred through the food webs and the Hg content in predators to be ultimately controlled by MeHg concentrations of the waters of their foraging zones. Many Mediterranean top-predatory fish still exceed European Union regulatory Hg thresholds. This emphasizes the necessity of monitoring the exposure of Mediterranean populations, to formulate adequate mitigation strategies and recommendations, without advising against seafood consumption. This review also points out other insufficiencies of knowledge of Hg cycling in the Mediterranean Sea, including temporal variations in air-sea exchange, hydrothermal and cold seep inputs, point sources, submarine groundwater discharge, and exchanges between margins and the open sea. Future assessment of global change impacts under the Minamata Convention Hg policy requires long-term observations and dedicated high-resolution Earth System Models for the Mediterranean region.

Prevalence of Heterotrophic Methylmercury Detoxifying Bacteria across Oceanic Regions.

Microbial reduction of inorganic divalent mercury (Hg2+) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg2+ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle.

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 (HgII) 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 HgII 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 HgII-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 HgII methylation is a bio-physico-chemical conundrum in which the efficiency of biological HgII methylation appears to depend chiefly on HgII 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.

Methanogenesis Is an Important Process in Controlling MeHg Concentration in Rice Paddy Soils Affected by Mining Activities.

Rice paddies are agricultural sites of special concern because the potent toxin methylmercury (MeHg), produced in rice paddy soils, accumulates in rice grains. MeHg cycling is mostly controlled by microbes but their importance in MeHg production and degradation in paddy soils and across a Hg concentration gradient remains unclear. Here we used surface and rhizosphere soil samples in a series of incubation experiments in combination with stable isotope tracers to investigate the relative importance of different microbial groups on MeHg production and degradation across a Hg contamination gradient. We showed that sulfate reduction was the main driver of MeHg formation and concentration at control sites, and that methanogenesis had an important and complex role in MeHg cycling as Hg concentrations increased. The inhibition of methanogenesis at the mining sites led to an increase in MeHg production up to 16.6-fold and a decrease in MeHg degradation by up to 77%, suggesting that methanogenesis is associated with MeHg degradation as Hg concentrations increased. This study broadens our understanding of the roles of microbes in MeHg cycling and highlights methanogenesis as a key control of MeHg concentrations in rice paddies, offering the potential for mitigation of Hg contamination and for the safe production of rice in Hg-contaminated areas.

Human health risk of methylmercury from fish consumption at the largest floodplain in Colombia.

Colombia is one of the countries with the highest emissions of mercury (Hg) to the environment, due to its use in gold mining. This study evaluated the human health risk from exposure to Hg through fish consumption in 11 municipalities located in the Mojana region, northern Colombia. The study participants (n = 839) were categorized into three population groups: children (CHD), women of childbearing age (WCHA) and the rest of population (RP). Total Hg (THg) and methylmercury (MeHg) concentrations were evaluated in the top ten most consumed fish species (n = 292). Median concentrations (range: 0.22-0.58 µg/g ww) of the five carnivorous fish species exceeded the reference limit established by FAO/WHO (0.2 µg/g ww) for vulnerable populations. For 6 of the 10 studied fish species, the estimated weekly intake (EWI) in children was above the provisional tolerable weekly intake (PTWI, 1.6 µg/kg bw/week) of MeHg established by JECFA. EWI values for WCHA were above PTWI in 4 fish species, whereas in general, for RP group values were below PTWI (3.2 µg/kg bw/week). Our assessment of potential risks to MeHg exposure indicated that most of the consumed fish could generate negative effects in vulnerable groups, because according to ingestion rate, MeHg permissible is, in some cases, up to 4 times higher than reference limits. Consumption advisories should be a guidance to avoid risk, gain nutritional benefits, and sustain fish populations. Because its high MeHg levels as well as high ingestion, it is recommended that inhabitants of this region should stop eating certain kinds of fish and the whole fish as a single meal. To reduce its harmful intake, we have proposed a didactic strategy based on marbles that control the portion of fish they are eating.

Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes.

Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCE Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.

Role of Settling Particles on Mercury Methylation in the Oxic Water Column of Freshwater Systems.

As the methylation of inorganic mercury to neurotoxic methylmercury has been attributed to the activity of anaerobic bacteria, the formation of methylmercury in the oxic water column of marine ecosystems has puzzled scientists over the past years. Here we show for the first time that methylmercury can be produced in particles sinking through oxygenated water column of lakes. Total mercury and methylmercury concentrations were measured in the settling particles and in surface sediments of the largest freshwater lake in Western Europe (Lake Geneva). While total mercury concentration differences between sediments and settling particles were not significant, methylmercury concentrations were about ten-fold greater in settling particles. Methylmercury demethylation rate constants (kd) were of similar magnitude in both compartments. In contrast, mercury methylation rate constants (km) were one order of magnitude greater in settling particles. The net potential for methylmercury formation, assessed by the ratio between the two rate constants (km kd-1), was therefore up to ten fold greater in settling particles, denoting that in situ transformations likely contributed to the high methylmercury concentration found in settling particles. Mercury methylation was inhibited (∼80%) in settling particles amended with molybdate, demonstrating the prominent role of biological sulfate-reduction in the process.

Genomic and transcriptomic characterization of methylmercury detoxification in a deep ocean Alteromonas mediterranea ISS312.

Methylmercury (MeHg) is one of the most worrisome pollutants in marine systems. MeHg detoxification is mediated by merB and merA genes, responsible for the demethylation of MeHg and the reduction of inorganic mercury, respectively. Little is known about the biological capacity to detoxify this compound in marine environments, and even less the bacterial transcriptional changes during MeHg detoxification. This study provides the genomic and transcriptomic characterization of the deep ocean bacteria Alteromonas mediterranea ISS312 with capacity for MeHg degradation. Its genome sequence revealed four mer operons containing three merA gene and two merB gene copies, that could be horizontally transferred among distant related genomes by mobile genetic elements. The transcriptomic profiling in the presence of 5 µM MeHg showed that merA and merB genes are within the most expressed genes, although not all mer genes were equally transcribed. Besides, we aimed to identify functional orthologous genes that displayed expression profiles highly similar or identical to those genes within the mer operons, which could indicate they are under the same regulatory controls. We found contrasting expression profiles for each mer operon that were positively correlated with a wide array of functions mostly related to amino acid metabolism, but also to flagellar assembly or two component systems. Also, this study highlights that all merAB genes of the four operons were globally distributed across oceans layers with higher transcriptional activity in the mesopelagic deeper waters. Our study provides new insights about the transcriptional patterns related to the capacity of marine bacteria to detoxify MeHg, with important implications for the understanding of this process in marine ecosystems.

Unmasking the physiology of mercury detoxifying bacteria from polluted sediments.

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

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.

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.

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

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

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-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) 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 coassembly 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 coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

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.

Occupational human exposure to mercury in artisanal small-scale gold mining communities of Colombia.

With the aim of protecting human life and the environment, the Minamata Convention seeks to reduce and monitor mercury (Hg) concentrations in the environment. Artisanal and Small-scale Gold Mining (ASGM) has been identified as the most important anthropogenic source of Hg at a global scale and an important route of human exposure to Hg. In this context, this study assessed total Hg (THg) in blood, urine and hair, and methylmercury (MeHg) in human hair samples from 238 participants with occupational exposure to Hg in the most relevant ASGM communities of Colombia. Mercury concentrations in different biological matrices were related to several variables of interest such as age, gender, body mass index, fish consumption, exposure time, and specific occupational activities, such as amalgamation and amalgam burning. The median values of THg in blood (3.70 µg/L), urine (4.00 µg/L) and hair (1.37 mg/kg), and hair MeHg (1.47 mg/kg) for all participants were below permissible concentrations set by WHO. However, about 40% of the miners showed Hg concentrations in blood, urine and/or hair above the WHO thresholds. In all the biological matrices studied, miners burning amalgams showed significantly higher concentrations than miners who did not burn amalgams, with values 7-, 7-, and 8-fold higher in blood, urine and hair, respectively. A multiple linear regression model revealed that burning amalgam and fish consumption were significant predictors of Hg exposure in miners. Miners from Guainía had the highest concentrations in urine and hair, most likely due to the high manipulation and burning of amalgam, and a high fish consumption. In contrast, miners from Caldas showed the lowest Hg concentrations in all the biomarkers because they do not manipulate or burn amalgam, as well as reporting the lowest fish consumption. Our study also highlighted that gold miners exposure to Hg depends on their work practices. Therefore, the implementation of a health education programme on gold mining strategies is required, especially in Guaina, Vaupés, Córdoba, and Antioquia departments.

Anaerobic and aerobic biodegradation of soil-extracted dissolved organic matter from the water-level-fluctuation zone of the Three Gorges Reservoir region, China.

The biodegradation of dissolved organic matter (DOM) in natural environments is determined by its molecular composition and reactivity. Redox oscillations are common in the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR). As a consequence, the soil DOM released is degraded under both anaerobic and aerobic conditions. The DOM compounds available for degradation under contrasting redox conditions and the resulting DOM composition still need to be elucidated. By combining laboratory experiments with an in-depth characterization of DOM optical properties, we show that different pathways controlled the depletion and enrichment of the DOM optical components under different oxygen regimes. In particular, 28-day dark biodegradation assays showed that up to 39.5 ± 4% DOM was degraded under anaerobic conditions, while 55.5 ± 6% DOM was biodegraded under aerobic conditions. Aerobic biodegradation resulted in a higher aromaticity and degree of humification of the DOM compared to anaerobic degradation. The specific UV absorbance at a wavelength of 254 (SUVA254) and biological index (BIX) could be used to track DOM biodegradation under anaerobic conditions. Under aerobic conditions, the SUVA254, BIX and concentration of coloured DOM (CDOM, reflected by a (355)) could track DOM biodegradation, and significant amounts of CDOM could be aerobically biodegraded.

Towards women-inclusive ecology: Representation, behavior, and perception of women at an international conference.

Conferences are ideal platforms for studying gender gaps in science because they are important cultural events that reflect barriers to women in academia. Here, we explored women's participation in ecology conferences by analyzing female representation, behavior, and personal experience at the 1st Meeting of the Iberian Society of Ecology (SIBECOL). The conference had 722 attendees, 576 contributions, and 27 scientific sessions. The gender of attendees and presenters was balanced (48/52% women/men), yet only 29% of the contributions had a woman as last author. Moreover, men presented most of the keynote talks (67%) and convened most of the sessions. Our results also showed that only 32% of the questions were asked by women, yet the number of questions raised by women increased when the speaker or the convener was a woman. Finally, the post-conference survey revealed that attendees had a good experience and did not perceive the event as a threatening context for women. Yet, differences in the responses between genders suggest that women tended to have a worse experience than their male counterparts. Although our results showed clear gender biases, most of the participants of the conference failed to detect it. Overall, we highlight the challenge of increasing women's scientific leadership, visibility and interaction in scientific conferences and we suggest several recommendations for creating inclusive meetings, thereby promoting equal opportunities for all participants.

Mercury cycling in freshwater systems - An updated conceptual model.

The widely accepted conceptual model of mercury (Hg) cycling in freshwater lakes (atmospheric deposition and runoff of inorganic Hg, methylation in bottom sediments and subsequent bioaccumulation and biomagnification in biota) is practically accepted as common knowledge. There is mounting evidence that the dominant processes that regulate inputs, transformations, and bioavailability of Hg in many lakes may be missing from this picture, and the fixation on the temperate stratified lake archetype is impeding our exploration of understudied, but potentially important sources of methylmercury to freshwater lakes. In this review, the importance of understudied biogeochemical processes and sites of methylmercury production are highlighted, including the complexity of redox transformations of Hg within the lake system itself, the complex assemblage of microbes found in biofilms and periphyton (two vastly understudied important sources of methylmercury in many freshwater ecosystems), and the critical role of autochthonous and allochthonous dissolved organic matter which mediates the net supply of methylmercury from the cellular to catchment scale. A conceptual model of lake Hg in contrasting lakes and catchments is presented, highlighting the importance of the autochthonous and allochthonous supply of dissolved organic matter, bioavailable inorganic mercury and methylmercury and providing a framework for future convergent research at the lab and field scales to establish more mechanistic process-based relationships within and among critical compartments that regulate methylmercury concentrations in freshwater ecosystems.