Metagenomics of a radioactive legacy site
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14718 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1527240_1.fastq.gz | Fastqsanger.gz | |||
| ERR1527240_2.fastq.gz | Fastqsanger.gz | |||
| ERR1527250_1.fastq.gz | Fastqsanger.gz | |||
| ERR1527250_2.fastq.gz | Fastqsanger.gz | |||
| ERR1527260_1.fastq.gz | Fastqsanger.gz |
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Project description:EMG produced TPA metagenomics assembly of the Study of the changes in the metagenome of the groundwater community at (Metagenomics of a radioactive legacy site) data set
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Project description:During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and ‘Candidatus Methanoperedenaceae’ (ANME-2D). Within the undescribed DPANN, the newly proposed orders ‘Ca. Gugararchaeales’, ‘Ca. Burarchaeales’ and ‘Ca. Anstonellales’, constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the ‘Ca. Micrarchaeota’ phylum compared to most other DPANN. The analysis of new and extant ‘Ca. Methanoperedens spp.’ MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most ‘Ca. Methanoperedens’ also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and ‘Ca. Methanoperedens’, while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
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Project description:Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. We analyzed soil metatranscriptomes, determining for the first time how fire and fire legacy interactively affect metabolically-active soil taxa, the microbial regulation of important carbon (C), nitrogen (N) and phosphorus (P) cycling, expression of carbohydrate-cycling enzyme pathways, and functional gene co-expression networks. Experimental fire strongly downregulated fungal activity while upregulating many bacterial and archaeal phyla. Further, fire decreased soil capacity for microbial C and N cycling and P transport, and drastically rewired functional gene co-expression. Perhaps most importantly, we highlight a novel role of soil fire legacy in regulation of microbial C, N, and P responses to recent fire. We observed a greater number of functional genes responsive to the interactive effects of fire and fire legacy than those affected solely by recent fire, indicating that many functional genes respond to fire only under certain fire legacy contexts. Therefore, without incorporating fire legacy of soils, studies will miss important ways that fire shapes microbial roles in ecosystem functioning. Finally, we showed that fire caused significant downregulation of carbon metabolism and nutrient cycling genes in microbiomes under abnormal soil fire histories, producing a novel warning for the future: human manipulation of fire legacies, either indirectly through global change-induced fire intensification or directly through fire suppression, can negatively impact soil microbiome functional responses to new fires.
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Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 M-BM-5g of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray. A 3-chip study was performed, each corresponding to hybridization with 4 M-BM-5g of labelled antisense mRNA retrieved from a monitoring well of a contaminated site (site B). Each probe (760nt) on the microarray was synthesized in eight replicates, and a total of 5,707 random probes was used to determine the background noise. Groundwater samples were collected from a contaminated site (site B) from three monitoring wells (P1, P2 and P3). P1: well located upstream to the contamination source. P2: well in the contamination source. P3 : well located downstream to the contamination source.
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Project description:A functional microarray targeting 24 genes involved in chlorinated solvent biodegradation pathways has been developed and used to monitor the gene expression in a contaminated site (site B) under ERD (enhanced reductive dechlorination) treatment. The microarray format provided by NimbleGen and used in this study is 12x135K. 4 µg of labelled antisense mRNA from 3 groundwater samples were hybridized on the microarray.
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Project description:Radioactive waste containing a few grams of plutonium (Pu) was disposed between 1960 and 1968 in trenches at the Little Forest Burial Ground (LFBG), near Sydney, Australia. A water sampling point installed in a former trench has enabled the radionuclide content of trench water and the response of the water level to rainfall to be studied. The trench water contains readily measurable Pu activity (~12 Bq/L of (239+240)Pu in 0.45 ?m-filtered water), and there is an associated contamination of Pu in surface soils. The highest (239+240)Pu soil activity was 829 Bq/kg in a shallow sample (0-1 cm depth) near the trench sampling point. Away from the trenches, the elevated concentrations of Pu in surface soils extend for tens of meters down-slope. The broader contamination may be partly attributable to dispersion events in the first decade after disposal, after which a layer of soil was added above the trenched area. Since this time, further Pu contamination has occurred near the trench-sampler within this added layer. The water level in the trench-sampler responds quickly to rainfall and intermittently reaches the surface, hence the Pu dispersion is attributed to saturation and overflow of the trenches during extreme rainfall events, referred to as the 'bathtub' effect.
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Project description:The use of aqueous film-forming foams (AFFF) at fire-training areas (FTAs) has introduced into ground- and surface waters a complex mixture of per- and poly-fluorinated alkyl substances (PFAS). The toxicity of environmental PFAS mixtures to wildlife is not well understood and presents a knowledge gap that limits accurate risk assessment. To evaluate reproductive biomarker responses to complex environmental PFAS mixtures, we conducted a series of on-site experiments using flow-through mobile laboratories exposing fish to groundwater impacted by a legacy FTA and an adjacent reference site A 60K fathead minnow microarray was used to quantify gene expression patterns in the testis and liver of fish exposed to water from Fire Training Area 1 and 2 relative to a reference site.
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Project description:<p>Anthropogenic activities cause the release of vast amounts of contaminants into the environment and thus also into surface- and groundwaters. Regulatory monitoring determines whether critical threshold concentrations are surpassed, by mostly occasional probing. This irregular testing, however, does not capture the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants in response to water flows. We report the detection and tracing of five contaminants in the 'Hainich Critical Zone Exploratory' (CZE) in central Germany, a monitoring site established for regular sampling of groundwater from different depths and locations along a hill-slope recharge area. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids), the latter being volatilised from wood burning in ovens, show phases of seasonal dynamics in line with their release mode. Further, and alongside legacy herbicides (simazine and the triazine transformation product hydroxypropazine) and the concurrent flame retardant and plasticiser TPP (triphenyl phosphate), mobilisation events emerge from periods of high precipitation and water flows. This investigation highlights the persistence and mobilization of anthropogenic contaminants even in pristine environments. It illustrates the importance of long-term research for understanding ecosystem processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time.</p><p><br></p><p><strong>MS2 data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS3533' rel='noopener noreferrer' target='_blank'><strong>MTBLS3533</strong></a>.</p><p><strong>MS1 data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS8433' rel='noopener noreferrer' target='_blank'><strong>MTBLS8433</strong></a>.</p>
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Project description:<p>Anthropogenic activities cause the release of vast amounts of contaminants into the environment and thus also into surface- and groundwaters. Regulatory monitoring determines whether critical threshold concentrations are surpassed, by mostly occasional probing. This irregular testing, however, does not capture the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants in response to water flows. We report the detection and tracing of five contaminants in the 'Hainich Critical Zone Exploratory' (CZE) in central Germany, a monitoring site established for regular sampling of groundwater from different depths and locations along a hill-slope recharge area. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids), the latter being volatilised from wood burning in ovens, show phases of seasonal dynamics in line with their release mode. Further, and alongside legacy herbicides (simazine and the triazine transformation product hydroxypropazine) and the concurrent flame retardant and plasticiser TPP (triphenyl phosphate), mobilisation events emerge from periods of high precipitation and water flows. This investigation highlights the persistence and mobilization of anthropogenic contaminants even in pristine environments. It illustrates the importance of long-term research for understanding ecosystem processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time.</p><p><br></p><p><strong>MS1 data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS8433' rel='noopener noreferrer' target='_blank'><strong>MTBLS8433</strong></a>.</p><p><strong>MS2 data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS3533' rel='noopener noreferrer' target='_blank'><strong>MTBLS3533</strong></a>.</p>
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