Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA19145 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR000281.fastq.gz | Fastqsanger.gz | |||
| SRR000282.fastq.gz | Fastqsanger.gz | |||
| SRR000283.fastq.gz | Fastqsanger.gz | |||
| SRR000284.fastq.gz | Fastqsanger.gz | |||
| SRR000285.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Coastal ocean metagenomes from Sapelo Island (Georgia, USA)
| PRJNA552566 | ENA
Project description:Thaumarchaeota Diversity in a Coastal Estuary near Sapelo Island, Georgia, USA
| PRJNA353050 | ENA
Project description:Saline water bacterioplankton communities from Sapelo Island, Georgia, California, USA metatranscriptome
| PRJNA366639 | ENA
Project description:Dean Creek (Sapelo Island, GA) Surface Water Environmental Sampling Metagenome
| PRJNA29039 | ENA
Project description:Bacterioplankton communities in seawater around Xiamen Island
| PRJNA254376 | ENA
Project description:Bacterioplankton communities in seawater around Xiamen Island
| PRJNA254200 | ENA
Project description:Excess phosphate loading shifts bacterioplankton community composition in oligotrophic coastal water microcosms over time
| PRJDB3316 | ENA
Project description:Spatial Variation of Coastal Bacterioplankton Community along a Nitrogen and Phosphorus Co-pollution Gradient
| PRJDB3389 | ENA
Project description:Marine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbMarine snow plays a central role in carbon cycling. It consists of organic particles and particle-associated (PA) microbial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions. ial communities that are embedded in a sugary matrix. Metaproteomic analysis offers the unique opportunity to gain unprecedented insight into the microbial community composition and biomolecular activity of environmental samples. In order to realize this potential for marine PA microbial communities, new methods of protein extraction must be developed. In this study, we used 1D-SDS-PAGEs and LC-MS/MS to compare the efficiency of six established protein extraction protocols for the their applicability of metaproteomic analyses of the PA microbial community in the North Sea. A combination of SDS-buffer extraction and bead beating resulted in the greatest number of identified protein groups. As expected, a metagenomic database of the same environmental sample increased the number of protein identification by approximately 50%. To demonstrate the application of our established protocol, particulate bacterioplankton samples collected during spring phytoplankton bloom in 2009 near the island Helgoland, were analysed by a GeLC-MS/MS-based metaproteomic approach. Our results indicated that there are only slight differences in the taxonomical distribution between free-living (FL) and PA bacteria but that the abundance of protein groups involved in polysaccharide degradation, motility and particle specific stress (oxygen limitation, nutrient limitation, heavy metal stress) is higher in the PA fractions.
2021-02-15 | PXD012699 | Pride