Marine sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA541355 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment. These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms. Ultimately, these data suggest that marine fungi could be as important in oceanic ecosystems as they are in freshwater environments.
2020-07-14 | GSE117831 | GEO
Project description:Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate.
2010-07-22 | GSE12323 | GEO
Project description:Aromatic compound degradation bacteria_Genome sequencing and assembly
| PRJNA876106 | ENA
Project description:Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate. For each experimental set, aRNA from NaphS2 was labelled Cy5 (experiment) or Cy3(control) with three biological replicates hybridized in duplicate. In addition, because of the size of the predicted genome of NaphS2, ORFs were divided into two separate array designs, designated set1 and set2, such that set1 and set2 represent two separate array designs (probe sets) to be treated separately in statistical analysis.
2010-07-21 | E-GEOD-12323 | biostudies-arrayexpress
Project description:Nitrogenase is the key enzyme involved in nitrogen fixation and uses low potential electrons delivered by ferredoxin or flavodoxin to reduce dinitrogen gas (N2) to produce ammonia and hydrogen. Although the phototrophic alphaproteobacterium Rhodopseudomonas palustris encodes many proteins that can reduce ferredoxin, the electron bifurcating FixABCX complex is the only one shown to support nitrogen fixation. To gain insight into why R. palustris is unable to use these other enzymes to reduce ferredoxin in the absence of FixABCX, we isolated a suppressor of R. palustris DfixC that allowed this strain to grow under nitrogen-fixing conditions. We found two mutations were necessary and sufficient to restore growth under nitrogen-fixing conditions in the absence of a functional FixABCX. One mutation was in the primary ferredoxin involved in nitrogen fixation, fer1, and the other mutation was in rpa0678, a homolog of NAD+-dependent ferredoxin:NADPH oxidoreductase, which carries out flavin-based electron bifurcation to generate reduced Fd. We present evidence that Rpa0678 plays a role in electron transfer to benzoyl-CoA reductase, the key enzyme involved in anaerobic aromatic compound degradation. Together these findings indicate that the electron transfer pathway for anaerobic aromatic compound degradation was re-purposed to support nitrogen fixation in the suppressor strain.
2022-07-19 | GSE208087 | GEO
Project description:Microplastics represent a growing environmental concern for the oceans due to their potential capability to adsorb different classes of pollutants, thus representing a still unexplored source of exposure for aquatic organisms. In this study polystyrene (PS) microplastics were characterized for their capability to adsorb pyrene (PYR) as model compound for polycyclic aromatic hydrocarbons, and transfer this chemical to filter feeding mussels Mytilus galloprovincialis. Gene expression analyses of Mytilus galloprovincialis exposed to polystyrene (PS) microplastics and to polystyrene contaminated with pyrene (PS-PYR) have been performed trough a DNA microarray platform.
2014-12-27 | GSE57460 | GEO
Project description:Novosphingobium resinovorum strain SA1 is one of few strains capable of degrading sulfanilic acid which is a widely used representative of sulfonated aromatic compounds. In order to identify the elements involved in the biodegradation process and to understand the metabolic responces of the cells exposed to this aromatic compound, we performed a whole transcriptome analysis of cells grown on sulfanilic acid and glucose. Additionally, for distinguish the potential stress/starvation effects of the xenobiotic we compared the transcript profiles of samples taken from both the exponential and stationary growth phases.
2017-08-15 | GSE102626 | GEO
Project description:The degradation of aromatic compounds comprises an important step in the removal of pollutants and re-utilization of plastics and other non-biological polymers. Here we set out to study Pseudomonas sp. strain phDV1, a gram-negative bacterium that was selected for its ability to degrade aromatic compounds. In order to understand how the aromatic compounds and their degradation products are reintroduced in the metabolism of the bacteria and the systematic/metabolic response of the bacterium to the new carbon source, the proteome of this strain was analysed in the presence of succinate, phenol and o-, m-, p-cresol as sole carbon source. We then applied label-free quantitative proteomics to monitor overall proteome remodeling during metabolic adaptation to different carbon sources. As a reference proteome, we grew the bacteria in succinate and then compared the respective proteomes of bacteria grown on phenol and different cresols. In total, we identified 2295 proteins; 1908 proteins were used for quantification between different growth conditions. We found that 70, 100, 150 and 155 proteins were significantly differentially expressed in cells were grown in phenol, o-, m- and p-cresol-containing medium, respectively. The carbon source affected the synthesis of enzymes related to aromatic compound degradation, and in particular, the enzyme involved in the meta-pathway of monocyclic aromatic compounds degradation. In addition, proteins involved in the production of polyhydroxyalkanoate (PHA), an attractive biomaterial, showed higher expression levels in the presence of monocyclic aromatic compounds.Our results provide for the first time comprehensive information on the proteome response of this strain to monocyclic aromatic compounds.
2020-10-22 | PXD021237 | Pride
Project description:The genus Pseudomonas is a very versatile and heterogeneous group whose members regularly serve as model system of various applications. These include pathogens and rhizospheric strains as well as organisms with exceptional broad substrate ranges. Nevertheless, when it comes to physiological adaptation due to cell density and growth, on transcript- or proteome level, our knowledge is rather limited. The few existing studies so far focused mainly on B. subtilis and E. coli. In this study Pseudomonas putida F1, a model for the degradation of aromatic compounds, and its adaptation to stationary growth was investigated by label-free proteome quantification. The data unveiled that entrance to the stationary phase does not involve an abrupt switch within the P. putida F1 proteome, but is rather an ongoing adaptation which starts during exponential growth which is illustrated by principle component and functional enrichment analysis. These changes were especially metabolic adaptations, which involved a clear increase in amino acid degradation capabilities and a loss of transcription as well as translation capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. Finally, the data supports previous observations that phenylacetic acid concentrations might play an important role in growth and pathogenicity regulation within Pseudomonades.
2015-07-24 | PXD001219 | Pride