Amplicon Sequencing bacteria river sediments
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ABSTRACT:
PROVIDER: PRJEB39659 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil Aquifer Treatment (SAT) is recognized as a cost-effective approach to reduce contaminants of emerging concern (CECs) from Wastewater Treatment Plant (WWTP) effluents. However, its efficiency in removing the associated biological effects is still poorly understood. Here, we evaluated the efficiency of three pilot SAT systems, two of them enhanced with reactive barriers containing different proportions of sand and organic materials, in removing toxicity associated to CECs. SATs were fed with secondary effluents from the Palamós WWTP (N.E. Spain) during two consecutive campaigns scheduled before and after the summer of 2020. Fifteen water samples were collected from the WWTP effluent, below the barriers and 15 m into the aquifer. Transcriptomic analyses of zebrafish embryos exposed to the corresponding water extracts revealed a wide range of toxic activities in the WWTP effluents. Results demonstrated that the associated responses were reduced by more than 70% by SAT, achieving control levels in some cases. Similar results were obtained when human HepG2 hepatic cells were tested for cytotoxic and dioxin-like responses. Toxicity reduction appeared to be partially determined by the reactive barrier composition and/or SAT managing and was correlated with the removal of CECs by SAT. In conclusion, SAT appears to be a very promising approach for efficiently reducing the effects of recalcitrant pollutants from WWTP secondary effluents on the environment and human health.
2024-11-01 | GSE240250 | GEO
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoA-carrying AOA within these sediments.
2013-08-24 | GSE50163 | GEO
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoAÂ-carrying AOA within these sediments. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50163 | biostudies-arrayexpress
Project description:Columbia River Sediments Raw sequence reads
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Project description:Laboratory tests with marine flatfish were conducted to investigate associations among gene expression, higher biological responses and wastewater effluent exposure. Previous studies showed molecular responses such as elevated concentrations of plasma estradiol and vitellogenin in wild male hornyhead turbot (Pleuronichthys verticalis). In the present study, male hornyhead turbot were exposed to environmentally realistic (0.5%) and higher (5%) concentrations of chemically enhanced advanced-primary (PL) and full-secondary treated (HTP) effluents from two southern California wastewater treatment plants (WWTP). Hepatic gene expression was examined using a custom low-density microarray. <br><br>
2013-12-10 | E-MEXP-3851 | biostudies-arrayexpress
Project description:Yaojiang 2020 river sediments Raw sequence reads
| PRJNA909466 | ENA
Project description:Black yeast (Chaetothyriales) diversity in river sediments.
| PRJEB45768 | ENA
Project description:Longitudinal changes of microbial communities in water and sediments along Xiangjiang River
| PRJNA562110 | ENA
Project description:In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.
2025-09-15 | PXD057056 | Pride