Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589080 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils.
2009-12-15 | GSE19483 | GEO
Project description:Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multi-carbon alkanes have been recovered from archaeal cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here, we produced anoxic cultures degrading mid-chain petroleum n-alkanes from pentane (C5) to tetradecane (C14) at 70°C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
2025-07-07 | MTBLS7727 | MetaboLights
Project description:Aqueous-soluble hydrocarbons dissolve into the ocean’s interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism.
2025-02-27 | PXD052872 | Pride
Project description:<p>As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. In this study, we employed a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing and metabolomics, to analyze key differential genes, dominant microbial strains and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. The results show that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Pseudomonas, Rhodococcus and Brevundimonas remain dominant species in the rhizosphere microbiome. Additionally, when applying pantothenic acid, malic acid and citric acid selected from metabolomics to the oil sediment used for growing alfalfa, the degradation rates significantly improved, with pantothenic acid application resulting in approximately a 10% higher degradation rate compared to other treatments. Our findings offer essential insights for optimizing phytoremediation strategies and improving the efficiency of soil decontamination</p>
2025-05-16 | MTBLS11700 | MetaboLights
Project description:Traditional biomarkers for hydrocarbon exposure are not induced by all petroleum substances. The objective of this study was to determine if exposure to a crude oil and different refined oils would generate a common hydrocarbon-specific response in gene expression profiles that could be used as generic biomarkers of hydrocarbon exposure. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to the water accommodated fraction (WAF) of either kerosene, gas oil, heavy fuel oil, or crude oil for 96 hours. Tissue was collected for RNA extraction and microarray analysis. Exposure to each WAF resulted in a different list of differentially regulated genes, with few genes in common across treatments. Exposure to crude oil WAF changed the expression of genes including CYP1A and GST with known roles in detoxification pathways. These gene expression profiles were compared to others from previous experiments which used a diverse suite of toxicants. Clustering algorithms successfully i dentified gene expression profiles resulting from hydrocarbon exposure. These preliminary analyses highlight the difficulties of using single genes as diagnostic of petroleum hydrocarbon exposures. Further work is needed to determine if multivariate transcriptomic-based biomarkers may be a more effective tool than single gene studies for exposure monitoring of different oils. Two channel experiment; control versus exposed (samples were time matched). 3 biological replicates, three technical replicates for both exposed and control fish. Samples were paired at random. One replicate per array
2010-05-18 | E-GEOD-19483 | biostudies-arrayexpress
Project description:The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. The work in its entirety characterizes the transport, fate and catabolic activities of bacterial communities in petroleum-polluted soils and within plant tissues.
2020-04-10 | GSE148431 | GEO
Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.
2023-06-06 | GSE234088 | GEO
Project description:Microbial community diversity in petroleum reservoirs
| PRJNA246768 | ENA