Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Construction of protein-protein interaction network in sulfate-reducing bacteria: Unveiling of global response to Hg

Sulfate-reducing bacteria (SRB) play pivotal roles in the biotransformation of mercury (Hg). However, unrevealed global responses of SRB to Hg have restricted our understanding of details of Hg biotransformation processes. The absence of protein-protein interaction (PPI) network under Hg stimuli has been a bottleneck of proteomic analysis for molecular mechanisms of Hg transformation. This study constructed the first comprehensive PPI network of SRB in response to Hg, encompassing 67 connected nodes, 26 independent nodes, and 121 edges, covering 93% of differentially expressed proteins from both previous studies and this study. The network suggested that proteomic changes of SRB in response to Hg occurred globally, including microbial metabolism in diverse environments, carbon metabolism, nucleic acid metabolism and translation, nucleic acid repair, transport systems, nitrogen metabolism, and methyltransferase activity, partial of which could cover the known knowledge. Antibiotic resistance was the original response revealed by this network, providing insights into of Hg biotransformation mechanisms. This study firstly provided the foundational network for a comprehensive understanding of SRB's responses to Hg, convenient for exploration of potential targets for Hg biotransformation. Furthermore, the network indicated that Hg enhances the metabolic activities and modification pathways of SRB to maintain cellular activities, shedding light on the influences of Hg on the carbon, nitrogen, and sulfur cycles at the cellular level.

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.

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.

Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation

Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two Fe₄S₄ iron-sulfur clusters for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility in complex with the ligands, i.e., in their native states. Therefore, an apo-protein predicted by AF2 is actually a holo-protein awaiting ligands.

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.

Methylations in vitamin B12 biosynthesis and catalysis

Vitamin B₁₂ is an essential biomolecule that assists in the catalysis of methyl transfer and radical-based reactions in cellular metabolism. The structure of B₁₂ is characterized by a tetrapyrrolic corrin ring with a central cobalt ion coordinated with an upper ligand, and a lower ligand anchored via a nucleotide loop. Multiple methyl groups decorate B₁₂, and their presence (or absence) have structural and functional consequences. In this minireview, we focus on the methyl groups that distinguish vitamin B₁₂ from other tetrapyrrolic biomolecules and from its own naturally occurring analogues called cobamides. We draw information from recent advances in the field to understand the origins of these methyl groups and the enzymes that incorporate them, and discuss their biological significance.

Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria

Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.

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.

Mercury methylation upon coastal sediment resuspension: a worst-case approach under dark conditions

Mercury behavior upon resuspension of sediments from two impacted areas of Guanabara Bay was evaluated to assess worst-case methylmercury (MeHg) responses, under dark experimental conditions to prevent demethylation by photolysis. Study areas include the Rio de Janeiro Harbor (RJH) and the chlor-alkali plant-affected Meriti River (MR) estuary. Total mercury (THg) and MeHg concentrations were determined along 24-h experiments of sediment resuspension in the bay water in dark conditions. Fine-grained Meriti River (MR) estuary sediments had 8 times higher MeHg initial concentrations than sandy Rio de Janeiro Harbor (RJH) sediments (3.4 ± 0.29 vs. 0.41 ± 0.1 ng g^-1, respectively). Though THg contents were uncorrelated with resuspension time, statistically significant correlations of MeHg (r_s = 0.78) and %MeHg in relation to THg (r_s = 0.86) with resuspension time were observed for RJH sediments, indicating net methylation only for this study site. These positive correlation trends correspond to a 2.8 times MeHg concentration increase (ΔMeHg = 0.75 ng g^-1) and 4.4 times increase in %MeHg (Δ%MeHg = 1.0%), after 24 h of resuspension. This suggests that assessments of factors affecting the MeHg spatial-temporal variability and associated toxicity risks can be limited in some sites if concentration changes due to sediment resuspension-redeposition processes are not considered. Therefore, the inclusion of MeHg evaluation before and after sediment resuspension events is recommendable for the improvement of dredging licensing and monitoring activities.

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.

Roles of plant-associated microorganisms in regulating the fate of Hg in croplands: A perspective on potential pathways in maintaining sustainable agriculture

In heavy metal-contaminated croplands, plant-associated microorganisms play important roles in the adaptation of crops to heavy metals. Plant-associated microbes can interact with Hg and stimulate plant resistance to Hg toxicity, which is crucial for impeding Hg accumulation along the food chain. The roles of rhizosphere microorganisms for the improvement of plant growth and Hg resistance have drawn great research attention. However, the interactions among plant-endophyte-Hg have been neglected although they might be important for in vivo Hg detoxification. In this study, we systematically summarized 1) the roles of plant-associated microorganisms in Hg detoxification and plant growth, 2) Hg methylation and demethylation driven by plant-associated microbes, 3) the relationships between plant-associated microbes and Hg biogeochemical cycling. The possible mechanisms underlying crop-endophyte-Hg interactions were discussed, although limited studies on this aspect are available to date. The challenges and perspectives of plant-endophytes in dampening Hg phytotoxicity and controlling Hg accumulation in croplands were proposed on the basis of the present knowledge. Taken together, this work provides evidence for further understanding the interactions between soil-plant-endophyte-Hg systems and as well as new interpretations and perspectives into regulating the fate of Hg in croplands.

Microbial mercury transformations: Molecules, functions and organisms

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

Unravelling biogeochemical drivers of methylmercury production in an Arctic fen soil and a bog soil

Arctic tundra soils store a globally significant amount of mercury (Hg), which could be transformed to the neurotoxic methylmercury (MeHg) upon warming and thus poses serious threats to the Arctic ecosystem. However, our knowledge of the biogeochemical drivers of MeHg production is limited in these soils. Using substrate addition (acetate and sulfate) and selective microbial inhibition approaches, we investigated the geochemical drivers and dominant microbial methylators in 60-day microcosm incubations with two tundra soils: a circumneutral fen soil and an acidic bog soil, collected near Nome, Alaska, United States. Results showed that increasing acetate concentration had negligible influences on MeHg production in both soils. However, inhibition of sulfate-reducing bacteria (SRB) completely stalled MeHg production in the fen soil in the first 15 days, whereas addition of sulfate in the low-sulfate bog soil increased MeHg production by 5-fold, suggesting prominent roles of SRB in Hg(II) methylation. Without the addition of sulfate in the bog soil or when sulfate was depleted in the fen soil (after 15 days), both SRB and methanogens contributed to MeHg production. Analysis of microbial community composition confirmed the presence of several phyla known to harbor microorganisms associated with Hg(II) methylation in the soils. The observations suggest that SRB and methanogens were mainly responsible for Hg(II) methylation in these tundra soils, although their relative contributions depended on the availability of sulfate and possibly syntrophic metabolisms between SRB and methanogens.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

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

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