Potential for mercury methylation by Asgard archaea in mangrove sediments

Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment

Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g-1 dw d-1). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.

Simultaneous removal of methane and high nitrite from the wastewater by Methylomonas sp. with soluble methane monooxygenase

Aerobic methanotrophs play a crucial role in controlling methane emission in wastewater treatment. However, the high nitrite produced during ammonium oxidation, nitrate assimilation, and denitrification hinders methane oxidation and nitrogen removal. In this study, Methylomonas sp. HYX-M1, possessing two methane monooxygenase and multiple nitrite reductase genes, demonstrated efficient methane oxidation, coupled with nitrite removal abilities up to 6 mM. Strain HYX-M1 presented methane oxidation rate of 0.05 mmol/d and nitrite removal rate of 0.53 mM/d under low-oxygen conditions. Assimilation and denitrification mainly accounted for 94.6-96.06 % and 3.10-5.03 % of nitrite removal. Methane monooxygenase genes, pmoA and mmoX expressed in different nitrite concentrations. Meanwhile, the nirB and nirD of strain HYX-M1 upregulated by 2.7- and 8.5-fold in 6 mM, respectively. The sod and ahpC genes upregulated, contributing to the survival of strain HYX-M1 in high nitrite. These findings provide a new strategy for the application of aerobic methanotrophs in regulating methane emission of wastewater with high nitrite.

Mangroves increased the mercury methylation potential in the sediment by producing organic matters and altering microbial methylators community

Mangrove ecosystem has attracted global attention as a hotspot for mercury (Hg) methylation. Although numerous biotic and abiotic parameters have been reported to influence methylmercury (MeHg) production in sediments, the key factors determining the elevated MeHg levels in mangrove wetlands have not been well addressed. In this study, Hg levels in the sediments from different habitats (mudflats, mangrove fringe, and mangrove interior) in the Futian mangrove wetland were investigated, aiming to characterize the predominant factors affecting the MeHg production and distinguish the key microbial taxa responsible for Hg methylation. MeHg concentrations in the sediments from the mangrove interior (1.03 ± 0.34 ng g-1 dw) were significantly higher than those in mudflats (0.26 ± 0.08 ng g-1 dw) and mangrove fringe (0.45 ± 0.10 ng g-1 dw). Mangrove vegetation also promoted the accumulation of organic matters in sediments, which stimulated the growth of methylators, ultimately leading to an elevated MeHg level in the sediment. The data from 16S sequencing and random forest analysis further indicated that the increased abundances of Desulfococcus and Desulfosarcina, which belong to complete-oxidizing microbes with acetyl-CoA pathway and are favored by mangrove vegetation, were the primary contributors to MeHg production. Besides, syntrophic partners of methylators (e.g. Syntrophus) also play a considerable role in MeHg production. The present findings provide a deep understanding of Hg-methylation in mangrove wetlands, and offers valuable insights into of the interactions between mangrove plants and soil microbiome in the presence of Hg contamination.

Multiple effects of carbon, sulfur and iron on microbial mercury methylation in black-odorous sediments

Black-odorous sediments provide ideal conditions for microbial mercury methylation. However, the multiple effects of carbon, sulfur, and iron on the microbial methylmercury of mercury in black-odorous sediments remains unclear. In this study, we conducted mercury methylation experiments using sediments collected from organically contaminated water bodies, as well as black-odorous sediments simulated in the laboratory. The results showed that black-odorous sediments exhibit a high capacity for mercury methylation. By simulating the blackening and odorization process in sediments, it was confirmed that dissolved oxygen, organic matter and sulfide were the primary factors triggering the black-odorous phenomenon in sediments. Regarding the influence of key factors in sediments on methylmercury formation, the batch tests demonstrated that high concentrations of organics additions (above 200 mg/L) may reduce bacterial activity and weaken mercury methylation in sediments. Under five different iron-sulfur ratios, the concentrations of methylmercury in the black-odorous sediments showed an increasing trend, the ratio of 5.0 Fe/S exhibited the highest MeHg accumulation. The iron-sulfur ratio in the sediment had a significant effect on the mercury methylation process, which was mainly due to the competition between Fe2+ and Hg2+ for sulfide sites and the adsorption/coprecipitation of Hg2+ by FeS. These findings offer a potential avenue for further understanding and controlling mercury methylation, contributing to the mitigation of the potential threat of mercury pollution to the environment and human health.

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.

A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances

Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs shows that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.

Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments

Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.

Plastispheres as hotspots of microbially-driven methylmercury production in paddy soils

Microplastics (MPs) as emerging contaminants have accumulated extensively in agricultural ecosystems and are known to exert important effects on biogeochemical processes. However, how MPs in paddy soils influence the conversion of mercury (Hg) to neurotoxic methylmercury (MeHg) remains poorly understood. Here, we evaluated the effects of MPs on Hg methylation and associated microbial communities in microcosms using two typical paddy soils in China (i.e., yellow and red soils). Results showed that the addition of MPs significantly increased MeHg production in both soils, which could be related to higher Hg methylation potential in the plastisphere than in the bulk soil. We found significant divergences in the community composition of Hg methylators between the plastisphere and the bulk soil. In addition, the plastisphere had higher proportions of Geobacterales in the yellow soil and Methanomicrobia in the red soil compared with the bulk soil, respectively; and plastisphere also had more densely connected microbial groups between non-Hg methylators and Hg methylators. These microbiota in the plastisphere are different from those in the bulk soil, which could partially account for their distinct MeHg production ability. Our findings suggest plastisphere as a unique biotope for MeHg production and provide new insights into the environment risks of MP accumulation in agricultural soils.

MeHg production in eutrophic lakes: Focusing on the roles of algal organic matter and iron-sulfur-phosphorus dynamics

The mechanisms by which eutrophication affects methylmercury (MeHg) production have not been comprehensively summarized, which hinders accurately predicting the MeHg risk in eutrophic lakes. In this review, we first discussed the effects of eutrophication on biogeochemical cycle of mercury (Hg). Special attentions were paid to the roles of algal organic matter (AOM) and iron (Fe)-sulfur (S)-phosphorus (P) dynamics in MeHg production. Finally, the suggestions for risk control of MeHg in eutrophic lakes were proposed. AOM can affect in situ Hg methylation by stimulating the abundance and activities of Hg methylating microorganisms and regulating Hg bioavailability, which are dependent on bacteria-strain and algae species, the molecular weight and composition of AOM as well as environmental conditions (e.g., light). Fe-S-P dynamics under eutrophication including sulfate reduction, FeS formation and P release could also play crucial but complicated roles in MeHg production, in which AOM may participate through influencing the dissolution and aggregation processes, structural order and surface properties of HgS nanoparticles (HgS_NP). Future studies should pay more attention to the dynamics of AOM in responses to the changing environmental conditions (e.g., light penetration and redox fluctuations) and how such variations will subsequently affect MeHg production. The effects of Fe-S-P dynamics on MeHg production under eutrophication also deserve further investigations, especially the interactions between AOM and HgS_NP. Remediation strategies with lower disturbance, greater stability and less cost like the technology of interfacial O₂ nanobubbles are urgent to be explored. This review will deepen our understanding of the mechanisms of MeHg production in eutrophic lakes and provide theoretical guidance for its risk control.

New insights into sulfur input induced methylmercury production and accumulation in paddy soil and rice

Sulfur has a high affinity for mercury (Hg) and can serve as effective treating agent for Hg pollution. However, conflict effects between reducing Hg mobility and promoting Hg methylation by sulfur were found in recent studies, and there is a gap in understanding the potential mechanism of MeHg production under different sulfur-treated species and doses. Here, we investigated and compared the MeHg production in Hg-contaminated paddy soil and its accumulation in rice under elemental sulfur or sulfate treatment at a relatively low (500 mg·kg^-1) or high (1000 mg·kg^-1) level. The associated potential molecular mechanisms are also discussed with the help of density functional theory (DFT) calculation. Pot experiments demonstrate that both elemental sulfur and sulfate at high exposure levels increased MeHg production in soil (244.63-571.72 %) and its accumulation in raw rice (268.73-443.50 %). Coupling the reduction of sulfate or elemental sulfur and decrease of soil redox potential leads to the detachment of Hg-polysulfide complexes from the surface of HgS which can be explained by DFT calculations. Enhancement of free Hg and Fe release through reducing Fe(III) oxyhydroxides further promotes soil MeHg production. The results provide clues for understanding the mechanism by which exogenous sulfur promotes MeHg production in paddies and paddy-like environments and give new insights for decreasing Hg mobility by regulating soil conditions.

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

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