Seawater metagenome
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ABSTRACT:
PROVIDER: PRJNA309156 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This project presents field metaproteomics data from Trichodesmium colonies collected from the surface ocean. Most were collected from the tropical and subtropical Atlantic ocean, but there is also data from the long term Bermuda Atlantic Time Series and Hawaii Ocean Time Series. Trichodesmium is a globally important marine microbe and its growth and nitrogen fixation activity is limited by nutrient availability in the surface ocean. This dataset was generated to answer questions about limitations on Trichodesmium's growth and activity in the nature.
2020-05-08 | PXD016225 | Pride
Project description:Evidence of bacterioplankton community adaption in responses to long-term mariculture disturbance
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Project description:Temporal dynamics of bacterioplankton community in response to excessive nitrate loading in the oligotrophic coastal water
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Project description:In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.
2018-10-02 | GSE73987 | GEO
Project description:NYC aquatic vertebrate eDNA time series 2016
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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:Coastal Antarctic marine ecosystems play an important role in carbon cycling due to their highly productive seasonal phytoplankton blooms. Southern Ocean microbes are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12 ). Micronutrient limitation is a key driver of ecosystem dynamics and influences the composition of blooms, which are often dominated by either diatoms or the haptophyte Phaeocystis antarctica, each with varied impacts on carbon cycling. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remains poorly characterized. Using cultures, physiological analysis, and comparative ’omics we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12 , as previously suggested, and report new mechanistic insights of its B12 response in cultures of predominantly solitary and colonial cells. Proteomics coupled with proteogenomics detected a B12 -independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and is interreplaced with the B12 -dependent isoform (MetH) in replete conditions. Database searches returned homologs of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles and also bacterioplankton. Furthermore, MetE-fusion homologs were found to be expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12 -auxotrophic diatoms.
2023-02-27 | PXD031524 | Pride
Project description:Dynamics of eukaryotic and bacterial communities in coastal ecosystem
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Project description:Diel and daily coral reef seawater microbial time-series
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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