AquaDiva_Minimetagenomes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33610 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR3500138_1.fastq.gz | Fastqsanger.gz | |||
| ERR3500138_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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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>
2024-06-04 | MTBLS8433 | MetaboLights
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>
2024-06-04 | MTBLS3533 | MetaboLights
Project description:Roots were collected from young trees outplanted in three regions in Germany (Schorfheide, Swabian Alb, Hainich) and used for RNA extraction. In each region four plots were sampled. Two plants used from each plot. The RNA of the plants per plot was pooled. Four technical replicates were prepared.
2023-04-22 | E-MTAB-12854 | biostudies-arrayexpress
Project description:DNA derived fungal communities of terrestrial subsurface aquifers in Hainich CZE
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Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress
Project description:Background. Bacteria of the Candidate Phyla Radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways suggesting symbiotic life styles. Gracilibacteria (BD1-5) are part of the CPR branch, they possess alternate coded genomes and have two cultivated members that were shown to be microbial predators. However, besides genomic sampling, little is known about the lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, and particularly groundwater where they have initially been genomically resolved. The current study was set out with the aim of investigating the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany, to estimate their activity in situ and discern expressed genes involved in their lifestyle. Results. We coupled genome-resolved metagenomics and metaproteomics to investigate a microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered onto 0.2-μm and 0.1-μm filters to fraction CPR and other bacteria. Based on 670 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Galionellales and Gracilibacteria along with keystone microbes, low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations in their central metabolism but no co-occurrence to potential hosts. Their genomes encoded for a high number of proteins related to a predatory lifestyle, whose expression was detected in the proteome and included subunits related to type IV and type II secretion systems, as well as features related to cell-cell interactions and cell motility. Conclusion. We present a highly resolved analysis coupling metagenomics to metaproteomics for elucidating microbial dynamics of Gracilibacteria in groundwater. We posit that Gracilibacteria are successful microbial predators in this ecosystem potentially aiding in population control of this highly disturbed microbial community from the deep biosphere.
2024-08-08 | PXD042980 | Pride