Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea

Particulate mercury (Hg) dominates the microbially available Hg pool over dissolved Hg during the decay of marine diatom Chaetoceros debilis

Phytoplankton concentrate mercury (Hg) from surface water, significantly impacting microbial production and trophic transfer of the neurotoxin methylmercury (MeHg). However, the fate and microbial availability of phytoplankton-associated Hg are poorly understood. This study investigated variations of Hg species and their microbial availability during 42 days' decay experiments using the common marine diatom Chaetoceros debilis. During aerobic decay with irradiation and low-oxygen decay in dark, the majority of phytoplankton-associated Hg remained as particulate Hg (HgP) on debris, with less Hg released as dissolved Hg (HgD), as operationally defined by 0.22 μm filtration. Microbially available Hg, measured using an Escherichia coli-based biosensor under anoxic conditions, primarily originated from HgP (aerobic decay with irradiation: 75.2 ± 22.0 %; low-oxygen decay in dark: 76.6 ± 20.7 %). Besides, HgP demonstrated notably higher microbial availability at early decay stages, with 90.4 ± 1.2 % of HgP being absorbed by biosensors after 5 days' aerobic decay with irradiation. Considering Hg was predominantly associated with thiols in phytoplankton particles, this was mainly attributed to enhanced Hg ligand exchange between thiols on particles and microbial cell surfaces, facilitated by bacteria-particle attachment and interactions. The formation of less bioavailable Hg nanoparticles in phytoplankton-associated particles also contributed to varying microbial Hg availability. This study highlights the critical role of phytoplankton-associated HgP in microbial uptake, offering insights into MeHg production and related risks in aquatic environments.

Distribution and Environmental Preference of Potential Mercury Methylators in Paddy Soils across China

The neurotoxin methylmercury (MeHg) is produced mainly from the transformation of inorganic Hg by microorganisms carrying the hgcAB gene pair. Paddy soils are known to harbor diverse microbial communities exhibiting varying abilities in methylating inorganic Hg, but their distribution and environmental drivers remain unknown at a large spatial scale. Using hgcA gene amplicon sequencing, this study examined Hg-methylating communities from major rice-producing paddy soils across a transect of ∼3600 km and an altitude of ∼1300 m in China. Results showed that hgcA+ OTU richness was higher in tropical and subtropical paddy soils compared to temperate zones. Geobacteraceae, Smithellaceae, and Methanoregulaceae were identified as the dominant hgcA+ families associated with MeHg production, collectively accounting for up to 77% of total hgcA+ sequences. Hierarchical partitioning analyses revealed that pH was the main driver of hgcA genes from Geobacteraceae (14.8%) and Methanoregulaceae (16.3%), while altitude accounted for 21.4% of hgcA genes from Smithellaceae. Based on these environmental preferences, a machine-learning algorithm was used to predict the spatial distribution of these dominant hgcA+ families, thereby providing novel insights into important microbial determinants for improved prediction of MeHg production in paddy soils across China.

Impact of geochemistry and microbes on the methylmercury production in mangrove sediments

Unraveling the geochemical and microbial controls on methylmercury (MeHg) dynamics in mangrove sediments is important, as MeHg can potentially pose risks to marine biota and people that rely on these ecosystems. While the important role of sulfate-reducing bacteria in MeHg formation has been examined in this ecologically important habitat, the contribution of non-Hg methylating communities on MeHg production remains particularly unclear. Here, we collected sediment samples from 13 mangrove forests in south China and examined the geochemical parameters and microbial communities related to the Hg methylation. MeHg concentrations were significantly correlated to the OM-related parameters such as organic carbon content, total nitrogen, and dissolved organic carbon concentrations, suggesting the importance of OM in the MeHg production. Sulfate-reducing bacteria were the major Hg-methylators in mangrove sediments. Desulfobacteraceae and Desulfobulbaceae dominated the Hg-methylating microbes. Classification random forest analysis detected strong co-occurrence between Hg methylators and putative non-Hg methylators, thus suggesting that both types of microorganisms contribute to the MeHg dynamics in the sediments. Our study provides an overview of MeHg contamination in south China and advances our understanding of Hg methylation in mangrove ecosystems.

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

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.

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.

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation

Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.

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.

Cross-shelf processes of terrigenous organic matter drive mercury speciation on the east siberian shelf in the Arctic Ocean

The cross-shelf distributions of total mercury (THg), methylmercury (MeHg) and organic and inorganic matter, as well as the presence of the hgcA gene were investigated on the East Siberian Shelf (ESS) to understand the processes underlying the speciation of sedimentary Hg. Samples were collected from 12 stations grouped into four zones based on water depth: inner shelf (5 stations), mid-shelf (3 stations), outer shelf (2 stations), and slope (2 stations). The THg concentration in the surface sediment increased from the inner shelf (0.25 ± 0.023 nmol g-1) toward the slope (0.52 nmol g-1), and, when normalized to total organic carbon content, the THg showed a positive correlation with the clay-to-sand ratio (r2 = 0.48, p = 0.012) and degree of chemical weathering (r2 = 0.79, p = 0.0001). The highest MeHg concentrations (3.0 ± 1.8 pmol g-1), as well as peaks in the S/C ratio (0.012 ± 0.002) of sediment-leached organic matter, were found on the mid-shelf, suggesting that the activities of sulfate reducers control the net Hg(II) methylation rates in the sediment. This was supported by results from a principal component analysis (PCA) performed with Hg species concentrations and sediment-leached organic matter compositions. The site-specific variation in MeHg showed the highest similarity with that of CHONS compounds in the PCA, where Deltaproteobacteria were projected to be putative Hg(II) methylators in the gene analysis. In summary, the hydrodynamic sorting of lithogenic particles appears to govern the cross-shelf distribution of THg, and in situ methylation is considered a major source of MeHg in the ESS sediment.

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.

Potential for mercury methylation by Asgard archaea in mangrove sediments

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

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

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

Anaerobic mercury methylators inhabit sinking particles of oxic water columns

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

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.

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.

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.

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

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

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

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

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

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

An In Situ Study to Understand Community Structure of Estuarine Microbes on the Plastisphere

Microplastics are defined as pieces of plastic that are smaller than 5 mm and they are now considered one of the most abundant ubiquitous plastic debris. Microbial communities that settle on particles can potentially lead to the transport of pathogenic and harmful bloom-forming species, as well as have an impact on global biogeochemical cycles. However, little is known about the acclimation of microbes to different types of microplastic in the estuarine environment. In this study, 16S ribosomal RNA sequencing and analysis was performed on biofilm samples from three different types of microplastic beads placed in Baltimore’s Inner Harbor. Microbial communities associated with microplastic particles and glass bead control were monitored throughout the 28-day incubation time. A significant taxonomic composition dissimilarity was observed between particles-associated and free-living communities, suggesting a unique microbial adaptation to these biofilms. The polymer types, however, did not significantly influence the microbial community composition. Some families with interesting potential metabolism were identified in the plastisphere samples, including Cyanobacteria, Planctomycetes, Desulfobacteriota, and Firmicutes, leading into speculation of their ecological responses and metabolic roles in the estuarine environment. It is crucial to understand the microorganisms that inhabit plastic debris in estuarine systems and their potential metabolic capacity and how it may differ from its marine counterparts in order to assess their roles in global nutrient cycles and if they have ability to be utilized in bioremediation for plastic pollution.

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.

Effects and mechanisms of organic matter regulating the methylmercury dynamics in mangrove sediments

Mangrove ecosystems serve as an important carbon sink but also could be a hotspot that produces neurotoxic methylmercury (MeHg). Although many studies have focused on mercury (Hg) contamination in this carbon-rich ecosystem, our understanding of the effects and mechanisms of the organic matter (OM) regulation of MeHg production in mangrove sediments is still limited. Here, we examined the effects of Hg contamination and OM enrichment on MeHg production in anoxic mangrove sediments and identified the major microbial guilds attending this process. The mangrove sediments possessed a high potential for producing MeHg, but this was counterbalanced by its rapid degradation. Sulfate-reducing bacteria (SRB) such as Desulfobacterales, Desulfovibrionales, and Syntrophobacterales were the major methylators. OM diagenesis significantly changed the biogeochemical conditions, accelerating MeHg degradation in the sediments. The enhanced MeHg degradation could be attributed to the abundant sulfide produced during OM decomposition, which could potentially inhibit the Hg methylation by immobilization of inorganic Hg, abiotically degrade MeHg, and favor the non-mer-mediated degradation of MeHg by SRB. Our study provides both geochemical and microbial clues that can partly explain the low MeHg levels widely observed in mangrove sediments.

Particle-Bound Hg(II) is Available for Microbial Uptake as Revealed by a Whole-Cell Biosensor

Particle-bound mercury (Hg_P), ubiquitously present in aquatic environments, can be methylated into highly toxic methylmercury, but it remains challenging to assess its bioavailability. In this study, we developed anEscherichia coli-based whole-cell biosensor to probe the microbial uptake of inorganic Hg(II) and assess the bioavailability of Hg_P sorbed on natural and model particles. This biosensor can quantitatively distinguish the contribution of dissolved Hg(II) and Hg_P to intracellular Hg. Results showed that the microbial uptake of Hg_P was ubiquitous in the environment, as evidenced by the bioavailability of sorbed-Hg(II) onto particulate matter and model particles (Fe₂O₃, Fe₃O₄, Al₂O₃, and SiO₂). In both oxic and anoxic environments, Hg_P was an important Hg(II) source for microbial uptake, with enhanced bioavailability under anoxic conditions. The composition of particles significantly affected the microbial uptake of Hg_P, with higher bioavailability being observed for Fe₂O₃ and lower for Al₂O₃ particles. The bioavailability of Hg_P varied also with the size of particles. In addition, coating with humic substances and model organic compound (cysteine) on Fe₂O₃ particles decreased the bioavailability of Hg_P. Overall, our findings highlight the role of Hg_P in Hg biogeochemical cycling and shed light on the enhanced Hg-methylation in settling particles and sediments in aquatic environments.

Microbial mercury methylation potential in a large-scale municipal solid waste landfill, China

Landfills harbor ideal conditions for microbial mercury methylation. However, the levels and distribution of mercury (Hg) and methylmercury (MeHg), potential microbial Hg methylation, and their linkage within landfills are largely unknown. In the present study, total mercury (THg), MeHg, the Hg methylation gene (hgcA) and mer operon were quantified in 30 waste samples from different depths (0-30 m) at 5 locations within a large-scale landfill in China. The average concentrations of THg and MeHg in the solid waste samples were 1422.91 ng/g and 3.15 ng/g, respectively. THg (up to 14405.29 ng/g) and MeHg (up to 10.42 ng/g) have high concentrations in the middle part (10-15 m) along the depth profiles. The concentration of THg was strongly positively (both p < 0.05) correlated with the MeHg concentration and the relative abundance of hgcA, indicating that the THg concentration can play an important role in microbial Hg methylation. The hgcA genes were detected in most samples and mer operon were detected in all samples. Combined hgcA qPCR and metagenomics data showed that Archaea Methanofollis may mainly account for Hg methylation within landfills. These findings provide fundamental knowledge on Hg cycles in landfills.

Evaluating metagenomic assembly approaches for biome-specific gene catalogues

BACKGROUND

For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly.

RESULTS

The mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated. The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research.

CONCLUSION

The mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples. Video abstract.

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

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

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

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

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