Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biodegradation of PBAT: Tracking the assimilation of labelled carbon

ABSTRACT: The use of carbon labelled PBAT units allowed us to follow biodegradation of all PBAT building blocks. The presented workflow is a novel approach to study the fundamental steps in polymer biodegradation in complex systems.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Metagenome

SUBMITTER: Jan Struckmann Poulsen

LAB HEAD: Jeppe Lund Nielsen

PROVIDER: PXD039265 | Pride | 2023-07-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AA000_JSP_JLN_UPLIFT.idXML	Other
	AA000_JSP_JLN_UPLIFT.mzML	Mzml
	AA006_JSP_JLN_UPLIFT.idXML	Other
	AA006_JSP_JLN_UPLIFT.mzML	Mzml
	AA024_JSP_JLN_UPLIFT_20221214012024.idXML	Other

Items per page:

1 - 5 of 46

Similar Datasets

Lignocellulose-rich residues in anaerobic digestion

Project description:In this study, a complex microbial community from a semi-continues reactor, which only substrate is wheat straw, was incubated in a batch experiment with 13C-cellulose. protein stable isotope probing (protein-SIP) was used to identify the organisms, at high taxonomic resolution, involved in the degradation of cellulose by tracking the incorporation of 13C in the newly synthetized proteins. Thereby providing information regarding identity and function simultaneously and enable the optimization of biotechnologies for biofuels production.

2023-11-30 | PXD036712 | Pride

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

Protein-SIP of cellulose-fed reactors

Project description:In this study we examined an anaerobic digester reactor fed with cellulose in order to identify cellulose degrading microorganisms using a culture independent approach. A metagenome was linked to the newly synthesized proteins involved by cellulose, by investigation of labelled proteins (Protein-SIP). The study aims at identifying microorganisms involved in the degradation of plant-based biomass.

2022-03-23 | PXD027303 | Pride

Biodegradation of PBAT: Tracking the assimilation of labelled carbon

Project description:Biodegradation of PBAT

| PRJEB58773 | ENA

MAA-SIP biomethanisation with hydrogen addition

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

Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments

Project description:Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium (Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13C-labelled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1 – 14.2%), labeling ratio (LR, 0.13 – 0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13C-labeled fungal metabolites into bacterial proteins. Distinct 13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).

2023-02-24 | PXD038571 | Pride

Proteomics of biphenyl labelling study

Project description:protein based stable isotope probing was performed for identifying microorganisms actually responsible for biphenyl biodegradation in soil environment.

2022-02-16 | PXD023646 | Pride

Anaerobic biodegradation

Project description:Biodegradation

| PRJEB19399 | ENA

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters

Project description:Inhibition of the anaerobic digestion process through accumulation of volatile fatty acids (VFA) is a recurring problem which is the result of unbalanced growth between acidogenic bacteria and methanogens. A speedy recovery is essential for an establishment of a feasible economical biogas productions. Yet, little is known regarding the organisms participating in the recovery. In this study the organisms involved in the recovery were studied using protein-stable isotope probing (Protein-SIP) and mapping this data onto a binned metagenome. Under acetate-accumulated simulating conditions a formation of 13C-labeled CO2 and CH4 was detected immediately after the addition of [U-13C]acetate, indicative of a high turnover rate of acetate. Several labeled peptides were detected in protein-SIP analysis. These 13C-labeled peptides were mapped onto a binned metagenome for improved taxanomical classification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia and one Bacteroidetes. The organisms affiliating with Clostridia and Bacteroidetes all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis; indicating that these organisms are possible syntrophic acetate-oxidizing bacteria (SAOB) that can facilitate acetate consumption via syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms involved in specific pathways.

2016-05-11 | PXD002996 | Pride

Investigating the autotrophic and mixotrophic metabolism of an anammox bacterium

Project description:Anaerobic ammonium oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome predictions. Here, we experimentally resolved the central carbon metabolism using metabolomics (LC-MS and GC-MS), metabolic flux analysis and proteomics (shot-gun proteomics).

2021-07-30 | PXD016171 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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