28 Search Results

Abstract Mercury (Hg) methylation genes ( hgcAB ) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in themore » environment. Furthermore, we introduce “marky‐coco”, a ready‐to‐use bioinformatic pipeline based on de novo single‐metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.« less

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuraciesmore » in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.« less

This record provides the data reported in Schwartz et al. "Incorporating Variable Sediment Microbial Activity into Methylmercury Production Kinetics Modeling".

Not provided.

In anoxic environments, anaerobic microorganisms carrying the hgcAB gene cluster can mediate the transformation of mercury (Hg) to methylmercury (MMHg). The kinetics of Hg transformation to MMHg in periphyton from East Fork Poplar Creek (EFPC) in Oak Ridge, TN have previously been modeled using a transient availability model (TAM). The TAM for Hg methylation combines kinetic expressions for processes that reduce Hg and MMHg availability for methylation and demethylation (multisite sorption of Hg and MMHg, Hg(II) reduction/Hg(0) oxidation) with methylation/demethylation kinetics. In this study, the TAM is used for the first time to describe MMHg production in sediment. We assessedmore » MMHg production in sediment microcosms using two different sediment types from EFPC: a carbon-rich sediment with lower, more anoxic redox potential and a sandy, carbon-poor sediment with a higher redox potential. Based on 16s rRNA sequencing, the overall microbial community structure in the two sediments was retained during the incubations. However, the hgcA containing methanogenic Euryarchaeota communities differed between sediment types and their growth followed different trajectories over the course of incubations, potentially contributing to the distinct patterns of MMHg production observed. The general TAM paradigm performed well in describing MMHg production in the sediments. However, the MMHg production and ancillary data suggested the need to revise the model structure to incorporate terms for variable microbial activity. We modified the TAM to include Monod-type kinetics for methylation and demethylation and observed an improved fit for the carbon-rich, microbially active sediment. Overall our work shows that the TAM can be applied to describe Hgmethylation in sediments and including expressions that account for variable microbial activity can improve the accuracy of the model description of the data in some cases.« less

We examined the composition and spatial correlation of sulfur and mercury pools in peatland soil profiles by measuring sulfur speciation by 1s X-ray absorption near-edge structure spectrocopy and mercury concentrations by cold vapor atomic fluorescence spectroscopy. Also investigated were the methylation/demethylation rate constants and the presence of hgcAB genes with depth. Methylmercury (MeHg) concentration and organic disulfide were spatially correlated and had a significant positive correlation (p < 0.05). This finding is consistent with these species being products of dissimilatory sulfate reduction. Conversely, a significant negative correlation between organic monosulfides and MeHg was observed, which is consistent with a reductionmore » in Hg(II) bioavailability via complexation reactions. Finally, a significant positive correlation between ester sulfate and instantaneous methylation rate constants was observed, which is consistent with ester sulfate being a substrate for mercury methylation via dissimilatory sulfate reduction. Furthermore, our findings point to the importance of organic sulfur species in mercury methylation processes, as substrates and products, as well as potential inhibitors of Hg(II) bioavailability. For a peatland system with sub-μmol L^–1 porewater concentrations of sulfate and hydrogen sulfide, our findings indicate that the solid-phase sulfur pools, which have a much larger sulfur concentration range, may be accessible to microbial activity or exchanging with the porewater.« less

We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species.

Desulfobulbus oligotrophicus Prop6 is a sulfate-reducing, propionate-oxidizing Deltabacterota (formerly Deltaproteobacteria) strain from sewage sludge. Desulfobulbus species are found in anoxic environments, in animal microbiota, and some produce the neurotoxin methylmercury. The 3.1-Mbp D. oligotrophicus genome sequence enables studies of diverse environmental adaptations and the evolutionary genomics of mercury methylation mechanisms.

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennessee (United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimentalmore » conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.« less

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 Pseudodesulfovibriomore » indicus J2T. Analysis of average nucleotide identity (ANI) of whole-genome sequences showed roughly 88 % ANI between P. hydrargyri BerOc1T and ND132T, and 84 % similarity between ND132T 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 : 1}ω9c 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.« less