Ocean water metagenome
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ABSTRACT:
PROVIDER: PRJNA808871 | ENA |
REPOSITORIES: ENA
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Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:Seamounts, often rising hundreds of metres above the surrounding seafloor, obstruct the flow of deep-ocean water. While the resultant entrainment of deep-water by seamounts is predicted from ocean circulation models, its empirical validation has been hampered by the large scale and slow rate of the interaction. To overcome these limitations we use the growth of planktonic bacteria to assess the interaction rate. The selected study site, Tropic Seamount, in the North-Eastern Atlantic represents the majority of isolated seamounts, which do not affect the surface ocean waters. We prove deep-water is entrained by the seamount by measuring 2.3 times higher bacterial concentrations in the seamount-associated or ‘sheath’ water than in deep-ocean water unaffected by seamounts. Genomic analyses of the dominant sheath-water bacteria confirm their planktonic origin, whilst proteomic analyses indicate their slow growth. According to our radiotracer experiments, the doubling time of sheath-water bacterioplankton is 1.5 years. Therefore, for bacterioplankton concentration to reach 2.3 times higher in the ambient seawater, the seamount would need to retain deep-ocean water for more than 3.5 years. We propose that turbulent mixing of the retained sheath-water could stimulate bacterioplankton growth by increasing the cell encounter rate with the ambient dissolved organic molecules. If some of these molecules chelate hydroxides of iron and manganese, bacterioplankton consumption of the organic chelators would result in precipitation of insoluble hydroxides. Hence precipitated hydroxides would form ferromanganese deposits as a result of the bacterioplankton-mediated deep-water seamount interaction.
2020-05-27 | PXD016702 | Pride
Project description:ocean water metagenomes from Western Pacific ocean and Bohai sea
| PRJNA739020 | ENA
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO