Revisiting mercury cycle in marine sediments: a potential multifaceted role for Desulfobacterota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB65319 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR11871000_1.fastq.gz | Fastqsanger.gz | |||
| ERR11871000_2.fastq.gz | Fastqsanger.gz | |||
| ERR11871001_1.fastq.gz | Fastqsanger.gz | |||
| ERR11871001_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 129 |
Similar Datasets
Project description:Neurotoxic methylmercury (MeHg) is produced by anaerobic Bacteria and Archaea possessing the genes hgcAB, but it is unknown how organic substrate and electron acceptor availability impacts the distribution and abundance of these organisms. We evaluated the impact of organic substrate amendments on mercury (Hg) methylation rates, microbial community structure, and the distribution of hgcAB+ microbes with sediments. Sediment slurries were amended with short-chain fatty acids, alcohols, or a polysaccharide. Minimal increases in MeHg were observed following lactate, ethanol, and methanol amendments, while a significant decrease (∼70%) was observed with cellobiose incubations. Postincubation, microbial diversity was assessed via 16S rRNA amplicon sequencing. The presence of hgcAB+ organisms was assessed with a broad-range degenerate PCR primer set for both genes, while the presence of microbes in each of the three dominant clades of methylators (Deltaproteobacteria, Firmicutes, and methanogenic Archaea) was measured with clade-specific degenerate hgcA quantitative PCR (qPCR) primer sets. The predominant microorganisms in unamended sediments consisted of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria Clade-specific qPCR identified hgcA+Deltaproteobacteria and Archaea in all sites but failed to detect hgcA+Firmicutes Cellobiose shifted the communities in all samples to ∼90% non-hgcAB-containing Firmicutes (mainly Bacillus spp. and Clostridium spp.). These results suggest that either expression of hgcAB is downregulated or, more likely given the lack of 16S rRNA gene presence after cellobiose incubation, Hg-methylating organisms are largely outcompeted by cellobiose degraders or degradation products of cellobiose. These results represent a step toward understanding and exploring simple methodologies for controlling MeHg production in the environment.IMPORTANCE Methylmercury (MeHg) is a neurotoxin produced by microorganisms that bioacummulates in the food web and poses a serious health risk to humans. Currently, the impact that organic substrate or electron acceptor availability has on the mercury (Hg)-methylating microorganisms is unclear. To study this, we set up microcosm experiments exposed to different organic substrates and electron acceptors and assayed for Hg methylation rates, for microbial community structure, and for distribution of Hg methylators. The sediment and groundwater was collected from East Fork Poplar Creek in Oak Ridge, TN. Amendment with cellobiose (a lignocellulosic degradation by-product) led to a drastic decrease in the Hg methylation rate compared to that in an unamended control, with an associated shift in the microbial community to mostly nonmethylating Firmicutes This, along with previous Hg-methylating microorganism identification methods, will be important for identifying strategies to control MeHg production and inform future remediation strategies.
| S-EPMC5772229 | biostudies-literature
Project description:The mechanisms of metal accumulation and toxicity in primary producers are not well understood. In a previous study (deposited in ArrayExpress archive under accession E-MTAB-892), we generated a dataset giving a fist insight into transcriptomic response of the aquatic macrophyte Elodea nuttallii to Hg and Cd exposure. In the present study we aimed to extend this investigation to different Hg-species, dose-response effects and multiple stress exposure. We therefore investigated the transcriptomic response of Elodea nuttallii to Hg, methyl-Hg, Cu and ultraviolet-B (UV-B) exposure. We applied different concentrations of Hg and methyl-Hg in order to study dose-response effects. Combined exposures of Hg and UV-B were conducted in order to assess interaction effects of multiple factors. Plants were exposed up to 24 h, RNA was extracted using Tri reagent, libraries prepared according to Illumina standard protocols and sequencing was done on Illumina HiSeq 2000. After quality check, raw sequence reads were assembled into contigs. About 160 Mbp assembled sequence information were generated in this study.
2014-06-30 | E-MTAB-2557 | biostudies-arrayexpress
Project description:Mercury (Hg) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are major environmental contaminants that commonly co-occur in the environment. Both Hg and TCDD are associated with a number of human diseases including cancers. While the individual toxicological effects of Hg and TCDD have been extensively investigated, studies on co-exposure are limited to a few genes and pathways. Therefore, a significant knowledge gap exists in the understanding of the deleterious effects of co-exposure to Hg and TCDD. Due to the prevalence of Hg and TCDD co-contamination in the environment and the major human health hazards they pose, it is important to obtain a fuller understanding of genome-wide effects of Hg and TCDD co-exposure. In this study, by performing a comprehensive transcriptomic analysis of human bronchial epithelial cells (BEAS-2B) exposed to Hg and TCDD individually and in combination, we have uncovered a subset of genes with altered expression only in the co-exposed cells. We also identified the additive as well as antagonistic effects of Hg and TCDD on gene expression. Moreover, we found that co-exposure impacted several biological and disease processes not affected by Hg or TCDD individually. Our studies show that the consequences of Hg and TCDD co-exposure on the transcriptional program and biological processes could be substantially different from single exposures, thus providing new insights into the co-exposure-specific pathogenic processes.
2017-02-27 | GSE83886 | GEO
Project description:Background and Methods: High mercury (Hg) levels are a significant concern in many aquatic environments, and adverse effects of Hg exposure in fish can include altered behavior, reproduction, growth, and increased stress responses. In addition, human health concerns over Hg continue to warrant new research on its mechanisms of action. The objectives of this study were to investigate the impacts of Hg on the female largemouth bass (LMB) central nervous system transcriptome by conducting a laboratory injection experiment with 2.5 µg/g body weight in addition to sampling LMB from an environment that contains high levels of Hg (St. Mary’s River, Florida, USA). These animals were compared to LMB that inhibit river systems with lower Hg (Big Wekiva, Santa Fe and St. John’s Rivers Florida, USA). A LMB 8 x 15 K microarray was used for hypothalamic (laboratory) and whole brain (field) transcriptomics analysis. Results: Mercury in the blood of LMB collected from St Mary’s River was significantly elevated 3-fold (~ 0.1 ng Hg/ml blood) compared to LMB collected from the other three sites (~ 0.03 ng Hg/ml blood). In the hypothalamus of Hg injected LMB, there were 937 genes that showed differential expression (raw p = 0.05) but there were no probes that passed an FDR for multiple hypothesis correction. In contrast, in field collected LMB there were 2909 genes that that showed differential expression (raw p = 0.05) of which 38 were significant after correction for multiple hypothesis testing (FDR = 0.05). These included Hsp90 co-chaperone Cdc37, multicopper oxidase, mismatch repair protein Msh6, and 16 kDa heat shock protein A. Functional enrichment in whole brains of LMB collected from the field sites revealed that genes involved in the biological processes of protein folding and targeting, regulation of protein metabolic process, and protein degradation (i.e. ubiquitin cycle) were over-represented. Interestingly, gene set enrichment analysis identifed expression targets that were in common between the laboratory experiment (MeHg injected) and field collected LMB and these consisted of mainly homeobox transcription factors (PROP paired-like homeobox 1, LIM homeobox 3 and paired-like homeodomain 1 and 2). Lastly, prevalent themes emerged in the SNEA expression targets that included neuropeptide receptor signaling, steroid signaling, and structural components, such as beta-actin, integrins, and stress fibres. Conclusions: This study characterizes novel cell signaling pathways that underlie Hg toxicity in the teleostean central nervous system.
2012-08-31 | GSE38458 | GEO
Project description:Background and Methods: High mercury (Hg) levels are a significant concern in many aquatic environments, and adverse effects of Hg exposure in fish can include altered behavior, reproduction, growth, and increased stress responses. In addition, human health concerns over Hg continue to warrant new research on its mechanisms of action. The objectives of this study were to investigate the impacts of Hg on the female largemouth bass (LMB) central nervous system transcriptome by conducting a laboratory injection experiment with 2.5 µg/g body weight in addition to sampling LMB from an environment that contains high levels of Hg (St. Mary’s River, Florida, USA). These animals were compared to LMB that inhibit river systems with lower Hg (Big Wekiva, Santa Fe and St. John’s Rivers Florida, USA). A LMB 8 x 15 K microarray was used for hypothalamic (laboratory) and whole brain (field) transcriptomics analysis. Results: Mercury in the blood of LMB collected from St Mary’s River was significantly elevated 3-fold (~ 0.1 ng Hg/ml blood) compared to LMB collected from the other three sites (~ 0.03 ng Hg/ml blood). In the hypothalamus of Hg injected LMB, there were 937 genes that showed differential expression (raw p = 0.05) but there were no probes that passed an FDR for multiple hypothesis correction. In contrast, in field collected LMB there were 2909 genes that that showed differential expression (raw p = 0.05) of which 38 were significant after correction for multiple hypothesis testing (FDR = 0.05). These included Hsp90 co-chaperone Cdc37, multicopper oxidase, mismatch repair protein Msh6, and 16 kDa heat shock protein A. Functional enrichment in whole brains of LMB collected from the field sites revealed that genes involved in the biological processes of protein folding and targeting, regulation of protein metabolic process, and protein degradation (i.e. ubiquitin cycle) were over-represented. Interestingly, gene set enrichment analysis identifed expression targets that were in common between the laboratory experiment (MeHg injected) and field collected LMB and these consisted of mainly homeobox transcription factors (PROP paired-like homeobox 1, LIM homeobox 3 and paired-like homeodomain 1 and 2). Lastly, prevalent themes emerged in the SNEA expression targets that included neuropeptide receptor signaling, steroid signaling, and structural components, such as beta-actin, integrins, and stress fibres. Conclusions: This study characterizes novel cell signaling pathways that underlie Hg toxicity in the teleostean central nervous system.
2012-08-31 | GSE38456 | GEO
Project description:Chemical analysis of the compounds present in sediment, although informative, often is not indicative of the downstream biological effects that these contaminants exert on resident aquatic organisms. More direct molecular methods are needed to determine if marine life is affected by exposure to sediments. In this study, we used an aquatic multispecies microarray and q-PCR to investigate the effects on gene expression in juvenile sea bream (Sparus aurata) of two contaminated sediments defined as sediment 1 and 2 respectively, from marine areas in Northern Italy.
2011-01-01 | E-TABM-1146 | biostudies-arrayexpress
Project description:Difference in mercuric ion removal by resting and growing cells of two mercury-resistant yeast strains, identified as Yarrowia spp. (strains Idd1 and Idd2), were studied. Resting cells of strain Idd2 exhibited high maximum Hg(2+) removal capacity (59 mg mercury per g dry cell weight [gdw(-1)]) by adsorption than those of resting cells of strain Idd1 (32 mg gdw(-1)). The resting cells of strain Idd2 exhibited a higher Hg(2+) desorption capacity using CaCl2 (68 %) and EDTA (48 %) than strain Idd1, depicting weaker binding of Hg(2+) onto strain Idd2 unlike strain Idd1. The actively growing yeast cells showed opposite Hg removal characteristics to those of the resting cells. Strain Idd1 adsorbed less Hg(2+) from culture medium supplemented with Hg(2+) than strain Idd2. However, the growing strain Idd1 reduced and vaporized 27 % of supplemented Hg(2+) as metallic mercury (Hg(0)), while the growing strains Idd2 vaporized 15 % of the supplemented Hg(2+). These two yeast strains are potential biotechnological tools for the eventual bioremediation of polluted aquatic systems.
| S-EPMC4375293 | biostudies-literature
Project description:Ocean sediments are the largest sink for mercury (Hg) sequestration and hence an important part of the global Hg cycle1. Yet accepted global average Hg flux data for deep-ocean sediments (> 200 m depth) are not based on measurements on sediments but are inferred from sinking particulates2. Mercury fluxes have never been reported from the deepest zone, the hadal (> 6 km depth). Here we report the first measurements of Hg fluxes from two hadal trenches (Atacama and Kermadec) and adjacent abyssal areas (2-6 km). Mercury concentrations of up to 400 ng g-1 were the highest recorded in marine sediments remote from anthropogenic or hydrothermal sources. The two trench systems differed significantly in Hg concentrations and fluxes, but hadal and abyssal areas within each system did not. The relatively low recent mean flux at Kermadec was 6-15 times higher than the inferred deep-ocean average1,3, while the median flux across all cores was 22-56 times higher. Thus, some hadal and abyssal sediments are Hg accumulation hot-spots. The hadal zone comprises only ~ 1% of the deep-ocean area, yet a preliminary estimate based on sediment Hg and particulate organic carbon (POC) fluxes suggests total hadal Hg accumulation may be 12-30% of the estimate for the entire deep-ocean. The few abyssal data show equally high Hg fluxes near trench systems. These results highlight a need for further research into deep-ocean Hg fluxes to better constrain global Hg models.
| S-EPMC8155115 | biostudies-literature
Project description:Methanogens and iron-reducing bacteria are major contributors to mercury methylation in boreal lake sediments
| PRJEB20960 | ENA
Project description:Adapting to changes in nutrient availability and environmental conditions is a fundamental property of cells. This adaptation requires a multi-directional coordination between metabolism, growth, and the cell cycle regulators (consisting of the family of cyclin-dependent kinases (CDKs), their regulatory subunits known as cyclins, CDK inhibitors, the retinoblastoma family members, and the E2F transcription factors). Deciphering the mechanisms accountable for this coordination is crucial for understanding various patho-physiological processes. While it is well established that metabolism and growth affect cell division, this review will focus on recent observations that demonstrate how cell cycle regulators coordinate metabolism, cell cycle progression, and growth. We will discuss how the cell cycle regulators directly regulate metabolic enzymes and pathways and summarize their involvement in the endolysosomal pathway and in the functions and dynamics of mitochondria.
| S-EPMC8359344 | biostudies-literature