Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Acidobacterial EPS degraders uraveled by stable isotope probing - Shotgun

ABSTRACT: Acidobacterial EPS degraders uraveled by stable isotope probing - Shotgun Metagenomics sequencing

PROVIDER: PRJEB31257 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

SIP of EPS degradation

Project description:Acidobacterial EPS degraders uraveled by stable isotope probing

| PRJEB29719 | ENA

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

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

DNA-SIP ETBE degraders

Project description:Stable isotope profiling of ETBE degraders

| PRJEB52346 | ENA

Identification of TBBPA-degraders in anaerobic bioreactor at environmentally relevant concentrations by combined protein-based stable isotope probing and metagenomics

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

Quantifying benthic bacterial activity under low oxygen using H218O stable isotope probing

Project description:Quantifying benthic bacterial activity under low oxygen using H218O stable isotope probing Raw sequence reads

| PRJNA498588 | ENA

Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing.

Project description: Not available

| S-EPMC5653698 | biostudies-literature

Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil.

Project description: Not available

| S-EPMC4551180 | biostudies-literature

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil contaminated aquifer by Pyro-SIP

2011-03-18 | GSE25449 | GEO

Stable isotope probing with 13C-labeled bicarbonate/proteomics of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada

Project description:In this work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.

2022-01-21 | PXD028578 | Pride

Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

Project description:Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota

| PRJNA489848 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data