Ontology highlight
ABSTRACT:
PROVIDER: PRJEB11870 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site. 2 samples examined from the different electron-acceptors (sulphate or ferric iron) incubates at the time point of maximal toluene degradation.
2011-03-18 | E-GEOD-25449 | biostudies-arrayexpress
Project description:By using metagenome resolved protein stable isotope probing (protein-SIP) through incubations of identical reactors with 13C labelled bicarbonate over a period of 48 hours, the study aims to map differences in the metabolic behaviour of the microbial community during anaerobic digestion.
2021-12-05 | PXD027519 | Pride
Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site.
2011-03-18 | GSE25449 | GEO
Project description:We developed an adaptation to Split-Pool Recognition of Interactions by Tag Extension (SPRITE) called SPRITE-immunoprecipitation (SIP), which enables us to map genome-wide higher-order interactions that are coupled with the protein of interest. In this study we generated SIP data fo H3K4me3 and pan-promoter mark. We generated SIP maps in two mammalian cell types – mouse embryonic stem cells (mES) and mouse bone marrow derived dendritic cells.
2020-08-18 | GSE156379 | GEO
Project description:Stable isotope probing of kangaroo forestomach content
| PRJNA230753 | ENA
Project description:The aim of this study was to identify TBBPA-degrading organisms in a complex microbial community by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). Firstly, the degradation kinetics were evaluated in order to simulate the decrease of residual mass of the labelled compound based on experimental data. In sequence, a metagenome was generated, and biomass was collected in different time-points for protein-SIP in incubations with 13C-TBBPA. This approach allowed for the identification organisms assimilating labelled carbon from the cometabolic degradation of a micropollutant.
2022-09-12 | PXD030335 | Pride
Project description:The limit of 15N detection in proteins of Pseudomonas putida was studied by LC-MS/MS. Cells were grown in the presence of 0.1%15N to 10% 15N.The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, demonstrating its high benefit in microbial ecology. The method’s high sensitivity allows the analysis of stable isotope distribution in target molecules, revealing metabolic activities of the species present in an ecosystem. Besides carbon, an application of protein-SIP with nitrogen is of interest for resolving the nitrogen fluxes in microbial communities. Thus, the sensitivity and reliability of a protein-SIP approach employing ^15 N was analyzed. For this, cultivations of Pseudomonas fluorescens ATCC 17483 with different ratios of ^14 N:^15 N were performed, from 10 % down to 0.1 % ^15 N. After incubation leading to complete labeling of biomass, proteins were extracted and separated by one-dimensional gel electrophoresis (1-DE), followed by tryptic digest and UPLC Orbitrap MS/MS analysis. ^15 N relative isotope abundance (RIA) was calculated based on isotopic patterns from identified peptides in mass spectra. The distribution of ^15 N RIA values among peptides was analyzed in samples with different ^15 N amount, and potential causes for variations within individual samples of either technical or biological origin were investigated. Using a number of 50 peptides, significant differences in ^15 N incorporation were found down to 0.1 % RIA. The study demonstrates that protein-SIP using ^15 N is sufficiently sensitive for quantitative investigation of microbial activity in nitrogen cycling processes. Raw data were processed for database search using Thermo Proteome Discoverer software (v1.0 build 43). Search was performed by tandem mass spectrometry ion search algorithms from the Mascot house server (v2.2.1). The following parameters were selected: /Pseudomonas fluorescens/ sequences of NCBInr (NCBI, version June 2012 and later) as criterion for taxonomy, tryptic cleavage, maximal two missed cleavage sites. A peptide tolerance threshold of ± 10 ppm and an MS/MS tolerance threshold of ± 0.2 Da were chosen. Carbamidomethylation at cysteines was given as static and oxidation of methionines as variable modification. Peptide identification data from all samples were merged using Thermo® Proteome Discoverer software (v1.0 build 43, Thermo Fisher Scientific). Only rank 1 peptides that reached a false-positive probability less than 0.05 in at least one sample were considered for further analysis.
2013-04-09 | PXD000127 | Pride