Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enrichment culture

ABSTRACT: Amplicon sequencing analysis of 16S rRNA gene of SCN-degrading consortium

PROVIDER: PRJDB7172 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR141366_1.fastq.gz	Fastqsanger.gz
	DRR141366_2.fastq.gz	Fastqsanger.gz
	DRR141367_1.fastq.gz	Fastqsanger.gz
	DRR141367_2.fastq.gz	Fastqsanger.gz
	DRR141368_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

enrichment culture

Project description:Amplicon sequencing analysis of 16S rRNA gene of DHS reactor

| PRJDB8576 | ENA

1,4-dioxane-degrading enrichment culture

Project description:Microbial community analyses of two 1,4-dioxane degrading consortia enriched from uncontaminated soils [16s rRNA]

| PRJNA382825 | ENA

Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors

Project description:Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers often utilize denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen-gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well-described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci. However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to highlight microbial drivers for lignocellulose transformation in woodchip bioreactors with the aim to provide an in-depth characterization of the indigenous microorganisms and their active enzymes. Our findings highlight a microbial community enriched for lignocellulose-degrading denitrifiers with key players from Giesbergeria, Cellulomonas, Azonexus, and UBA5070, including polysaccharide utilization loci from Bacteroidetes. A wide substrate specificity is observed among the many expressed carbohydrate active enzymes (CAZymes), evidencing a swift degradation of lignocellulose, including even enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

2024-10-21 | PXD050137 | Pride

Soil Metaproteomics LC-MS

Project description:Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of microbial populations (metaproteomics), yet not their genomic abundance (16S rRNA gene amplicon sequencing), supporting the hypothesis that metabolic activity may be more closely linked to climate than community composition.

2022-03-01 | PXD009773 | Pride

enrichment culture

Project description:Amplicon sequencing of Nitrotoga enrichment cultures

| PRJDB8089 | ENA

Desulfovibrio enrichment culture

Project description:Desulfovibrio enrichment culture degrading sulfonates

| PRJEB25655 | ENA

1,4-dioxane-degrading enrichment culture

Project description:SDIMO gene analysis of two 1,4-dioxane degrading consortia enriched from uncontaminated soils

| PRJNA382826 | ENA

Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics

Project description:In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.

2017-05-12 | PXD006118 | Pride

Mixed Culture

Project description:Bacterial consortium degrading Phenanthrene Raw sequence reads

| PRJNA562544 | ENA

naphthenic acid-degrading enrichment culture

Project description:NA-degrading consortia

| PRJNA390671 | ENA