Dataset Information

Metaprotemic analysis of groundwaters from a coal tar-contaminated aquifer in South Glens Falls, NY: MW37, Gel Slice

ABSTRACT: Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Prokaryotic Environmental Samples

SUBMITTER: Buck Hanson

LAB HEAD: Eugene Lewis Madsen

PROVIDER: PXD001035 | Pride | 2022-02-22

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	Hanson_Madsen_MW37_GelSlice_1.mgf	Mgf
	Hanson_Madsen_MW37_GelSlice_1_1.raw	Raw
	Hanson_Madsen_MW37_GelSlice_1_2.raw	Raw
	Hanson_Madsen_MW37_GelSlice_1_3.raw	Raw
	Hanson_Madsen_MW37_GelSlice_1_4.raw	Raw

Items per page:

1 - 5 of 9

Publications

In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer.

Hanson Buck T BT Madsen Eugene L EL

Environmental microbiology reports 20150224 2

Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragmen ...[more]

PMID: 25403415

Similar Datasets

Project description:During second generation biofuel production, optimization of cellulase activity is vital for synthesizing the end-product of anaerobic fermentation, bio-ethanol. The slightest change in pH, temperature, dissolved oxygen, carbon utilization, and addition or removal of essential supplements can reduce the secretion of necessary enzymes to degrade cellulosic biomass; resulting in a loss of free glucose. Determining the ecological effects of certain key media components is essential to understand how the bacterial or fungal colony will respond to a fluid cellulolytic environment. For our experiment a custom cellulosic media was designed to enhance the industrially important and recently isolated thermophile, Bacillus licheniformis YNP5-TSU. After several attempts to simplify the carboxymethylcellulose (CMC) media composition, impaired biofilm maturation and parallel declined cellulase activity was noticed. This negative artifact occurred during flask fermentation only when magnesium sulfate was removed from broth media. To analyze the shift in enzymatic gene expression, biofilm associated proteins were extracted and quantified through TMT10plex mass tag isobaric labeling of both magnesium sufficient (4.0mM MgSO4) and magnesium depleted media after 24hrs and 48hrs incubation periods. Raw data generated from nanoLC-MS/MS using an Orbitrap Fusion mass spectrometer identified over 2,000 proteins from both control and magnesium depleted samples when searched against the whole genome sequence of Bacillus licheniformis YNP5-TSU (NCBI accession number MEDD00000000). After statistical normalization and false discovery rate were calculated, 140 upregulated/downregulated expressed proteins were shown with 2σ significance to be effected by magnesium concentrations. In a closer look through STRING protein co-expression webs, over 15 were directly related to biofilm and cellulase activity, with fold changes as high as 5.78. Through this proteomic study of Bacillus licheniformis YNP5-TSU we are able to provide significant evidence that; (1) biofilm maturation and cellulase production are highly correlated and (2), their optimization is dependent upon by the addition of magnesium, an essential mineral for growth.