Browse
Submit Data
Databases
API
Help

Dataset Information

309 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic SIP of the soil communities

ABSTRACT: characterization of soil communities amended with 13C-methanol using proteomic SIP

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Uncultured Soil Bacterium S0137

SUBMITTER: Zhou Li

LAB HEAD: Chongle Pan

PROVIDER: PXD011739 | Pride | 2018-11-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Isolife_MeSIP_Day3Rep1_Elite_SIP_Run1.peptide.txt	Txt
	Isolife_MeSIP_Day3Rep1_Elite_SIP_Run1.protein.txt	Txt
	Isolife_MeSIP_Day3Rep1_Elite_SIP_Run1_01.raw	Raw
	Isolife_MeSIP_Day3Rep1_Elite_SIP_Run1_02.raw	Raw
	Isolife_MeSIP_Day3Rep1_Elite_SIP_Run1_03.raw	Raw

Items per page:

1 - 5 of 78

Similar Datasets

Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments

Project description:We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. The expression of distinct oxygenase-based catabolic pathways for toluene degradation was clearly apparent in 13C-labelled mRNA. We discuss how these direct insights into the gene expression and adaptation mechanisms within complex degrader communities can guide more integrated approaches in monitoring and restoration of contaminated sites.

2019-11-08 | GSE140055 | GEO

Multi-omics of the rhizosphere communities of Arabidopsis

Project description:characterization of rhizosphere communities of arabidopsis with metagenomics, metaproteomics and proteomic SIP

2018-11-21 | PXD011737 | Pride

Multi-omics of the rhizosphere communities of Maize - Part 1

Project description:characterization of rhizosphere communities of maize with metagenomics, metaproteomics and proteomic SIP

2018-11-30 | PXD011891 | Pride

Multi-omics of the rhizosphere communities of wheat - Part 2

Project description:characterization of rhizosphere communities of wheat with metagenomics, metaproteomics and proteomic SIP

2018-11-30 | PXD011892 | Pride

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

Project description:Stable isotope probing (SIP) has been used to track nu- trient flows in microbial communities, but existing pro- tein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identi- fies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences be- tween closely related protein sequences, and for detect- ing labeling patterns in low-abundance proteins or pro- teins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, 50%, and 98%. The method was then used to monitor incorporation of 15 N into established and regrow- ing microbial biofilms. The results indicate organism-spe- cific migration patterns from established communities into regrowing communities and provide insights into me- tabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13 C or 15 N in microbial communities. Molecular and Cellular Proteomics 10: 10.1074/mcp.M110.006049, 1–11, 2011.

2024-06-14 | PXD041958 | Pride

Multi-omics of the initial soil communites

Project description:characterization of soil communities with metagenomics and metaproteomics

2018-11-21 | PXD011738 | Pride

soil mcirobial functional communities

Project description:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant

2020-12-31 | GSE135153 | GEO

marine metagenome

Project description:13C methanol SIP (WCO station L4)

| PRJNA261236 | 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

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

2011-03-18 | GSE25449 | GEO