Columbia River coastal margin 'omics
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR864069_1.fastq.gz | Fastqsanger.gz | |||
| ERR864069_2.fastq.gz | Fastqsanger.gz | |||
| ERR864070_1.fastq.gz | Fastqsanger.gz | |||
| ERR864070_2.fastq.gz | Fastqsanger.gz | |||
| ERR864071_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:EMG produced TPA metagenomics assembly of the Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient (Columbia River coastal margin 'omics) data set
| PRJEB22509 | ENA
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.
2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress
Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212).
2010-09-10 | GSE18303 | GEO
Project description:Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (?=-0.664) and residence time (?=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.
| S-EPMC3965310 | biostudies-literature
Project description:Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches.
| S-EPMC2954162 | biostudies-other
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:Costa Rica Margin Subseafloor Microbial Community Analysis
| PRJEB11766 | ENA
Project description:In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.
2018-10-02 | GSE73987 | GEO
Project description:Glioblastoma recurrence originates from invasive cells that escape surgical resection, but their biology remains poorly understood. Here we generated three somatic mouse models recapitulating the main driver mutations of the human disease to characterise the infiltrative tumour margin. We find that, regardless of genetics, tumours are fuelled by highly proliferative glioma stem-like cells (GSCs) resembling active neural stem cells (NSCs), which recapitulate normal and injury-induced neurogenesis in both bulk and margin. Surprisingly, GSCs are evenly distributed across both regions, suggesting that invasive potential is uncoupled from stemness. However, tumour region influences fate choice, with margin cells progressing towards astrocyte-like, and bulk cells towards injured NSC-like (iNSCs) fates. iNSCs account for a significant proportion of dormant glioblastoma cells and are induced by interferon signalling within T-cell-rich niches that form selectively in the bulk. These findings identify key differences between bulk and margin and indicate that glioblastoma cell fate is under cell-extrinsic control.
2021-12-31 | GSE174470 | GEO
Project description:Multiple dam passage during seaward migration is thought to reduce the subsequent survival of Snake River Chinook salmon. This hypothesis developed because juvenile Chinook salmon from the Snake River, the Columbia River's largest tributary, migrate >700 km through eight hydropower dams and have lower adult return rates than downstream populations that migrate through only 3 or 4 dams. Using a large-scale telemetry array, we tested whether survival of hatchery-reared juvenile Snake River spring Chinook salmon is reduced in the estuary and coastal ocean relative to a downstream, hatchery-reared population from the Yakima River. During the initial 750-km, 1-mo-long migration through the estuary and coastal ocean, we found no evidence of differential survival; therefore, poorer adult returns of Snake River Chinook may develop far from the Columbia River. Thus, hydrosystem mitigation efforts may be ineffective if differential mortality rates develop in the North Pacific Ocean for reasons unrelated to dam passage.
| S-EPMC3637724 | biostudies-literature