Sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244781 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)
| PRJNA294625 | ENA
Project description:Combined effects of an Oil Spill, surfactant and solar radiation on surface marine microbiome in the Gulf of Mexico
2023-12-21 | PXD048022 | iProX
Project description:Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden. Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months. Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations. Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct. Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico. Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways. Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.
2016-12-06 | GSE90941 | GEO
Project description:In this study we characterize the gill transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Gill transcription was contrasted between doses and across timepoints following dosing.
2014-08-11 | E-MTAB-2834 | biostudies-arrayexpress
Project description:In this study we characterize the liver transcriptome changes in Gulf killifish (Fundulus grandis) that coincide with controlled laboratory-based exposure to various concentrations of experimentally-weathered south Louisiana crude oil. Liver transcription was contrasted between doses and across timepoints following dosing.
2014-08-13 | E-MTAB-2841 | biostudies-arrayexpress
Project description:Bathymodiolin mussels are a group of bivalves associated with deep-sea reducing habitats, such as hydrothermal vents and cold seeps. These mussels usually engage in an obligatory symbiosis with sulfur and/or methane oxidizing Gammaproteobacteria. In addition to these bacteria, Bathymodiolus heckerae that inhabit gas and oil seeps in Campeche Bay, the southern Gulf of Mexico, host bacteria phylogenetically with the Cycloclasticus genus. We recently discovered the capability for short-chain alkane degradation in draft genomes of symbiotic Cycloclasticus. With proteomics, we investigated whether the genes required for this process are expressed by the symbionts.
2016-12-05 | PXD005351 | Pride
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
2013-03-01 | GSE42286 | GEO
Project description:As apex predators, cetaceans are recognized as sentinels for the health of marine ecosystems. The ability to identify the impacts of anthropogenic contamination on the health of a species requires long term monitoring to establish baseline health parameters. This makes health measurements that can be sampled from free ranging animals highly desirable. In the current study, we investigate the utility of skin gene expression profiling to monitor the physiological, health, and contaminant exposure status in bottlenose dolphins. Remote integument biopsies were obtained from bottlenose dolphins at three locations in the northern Gulf of Mexico prior to oil exposure (May 2010) and during summer and winter of the two years (2010-2011) following their exposure to oil from the Deepwater Horizon oil spill. A bottlenose dolphin-specific oligonucleotide microarray was used to characterize the skin transcriptomes of 94 individuals from three genetically distinguishable populations in Barataria Bay, Louisiana, Chandeleur Sound, Louisiana, and Mississippi Sound, Mississippi. Location did not significantly affect the transcriptome patterns of the dolphins included in the study. In contrast, season had a profound effect on gene expression, with nearly one-third of all genes on the array differing significantly in expression between winter and the warmer seasons (p<0.01, fold-change >1.5). Gene ontology enrichment analysis revealed that processes related to cell proliferation, motility and differentiation dominated the seasonal differences in expression, which likely reflects the differences in ambient temperature to which the skin is exposed, and possibly changes in blood flow. More subtle differences were seen between spring and summer transcriptomes (1.5% differentially expressed), with two presumed oil-exposed animals presenting gene expression profiles more similar to the summer (exposed) animals than the other spring animals. Xenobiotic pathway components also showed some seasonal trends, which may reflect crosstalk between xenobiotic pathways and those regulating corticoids, hormones, and cytokines. Seasonal effects have not previously been considered in studies assessing gene expression in cetaceans, but clearly must be taken into account when applying transcriptomic analyses to investigate their exposure or health status.
2016-11-29 | GSE58471 | GEO
Project description:Bathymodiolus childressi is a species of deep-sea mussels found predominantly in the Gulf of Mexico. It colonizes cold seeps such as brine pool and oil seeps. The success of these animals in such environment is thought to be due to the symbiotic association of the mussel host with several species of bacteria. The aim of this study is to understand the role of the different partners involved in the symbiotic system using various “-omics” approaches. In addition to protein identification we used the mass spectrometry data generated and submitted with this project to derive the stable carbon isotope ratios for the different members of the symbiosis using the direct Protein-SIF method. The respective isotope pattern file and SIF computation files are included with this submission.
2020-02-27 | PXD008089 | Pride
Project description:Methane-oxidizing microbial communities from mesocosms in the Gulf of Mexico - GOM15C Gulf of Mexico metagenome
| PRJNA365099 | ENA