Seawater metagenome
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REPOSITORIES: ENA
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Project description:Excess phosphate loading shifts bacterioplankton community composition in oligotrophic coastal water microcosms over time
| PRJDB3316 | ENA
Project description:Long-term time series of bacterioplankton dynamics in coastal ocean
| PRJNA309156 | ENA
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:Dynamics of eukaryotic and bacterial communities in coastal ecosystem
| PRJDB12951 | ENA
Project description:Estuarine and coastal water Targeted loci environmental
| PRJNA284317 | ENA
Project description:Seasonal Dynamics of a Coastal Ecosystem Reveals Distinct Dynamics for Eukaryotes, Prokaryotes and Viral Communities
| PRJDB10706 | ENA
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:<p>Marine dissolved organic matter (DOM) varies in its recalcitrance to rapid microbial degradation. DOM of varying recalcitrance can be exported from the ocean surface to depth by subduction or convective mixing and oxidized over months to decades in deeper seawater. Carboxyl-rich alicyclic molecules (CRAM) are characterized as a major component of recalcitrant DOM throughout the oceanic water column. The oxidation of CRAM-like compounds may depend on specific bacterioplankton lineages with oxidative enzymes capable of catabolizing complex molecular structures like long-chain aliphatics, cyclic alkanes, and carboxylic acids. To investigate the interaction between bacteria and CRAM-like compounds, we conducted microbial remineralization experiments using several compounds rich in carboxyl groups and/or alicyclic rings, including deoxycholate, humic acid, lignin, and benzoic acid, as proxies for CRAM. Mesopelagic seawater (200 m) from the northwest Sargasso Sea was used as media and inoculum and incubated over 28 days. All amendments demonstrated significant DOC removal (2 – 11 µmol C L-1) compared to controls. Bacterioplankton abundance increased significantly in the deoxycholate and benzoic acid treatments relative to controls, with fast-growing <em>Spongiibacteracea</em>, <em>Euryarcheaota</em>, and slow-growing SAR11 enriched in the deoxycholate treatment and fast-growing <em>Alteromonas</em>, <em>Euryarcheaota</em>, and <em>Thaumarcheaota</em> enriched in the benzoic acid treatment. In contrast, bacterioplankton grew slower in the lignin and humic acid treatments, with oligotrophic SAR202 becoming significantly enriched in the lignin treatment. Our results indicate that the character of the CRAM proxy compounds resulted in distinct bacterioplankton removal rates and affected specific lineages of bacterioplankton capable of responding.</p>
2024-02-20 | MTBLS3512 | MetaboLights
Project description:Successional trajectories of coastal bacterioplankton communities in response to co-exposure of cadmium and phenanthrene
| PRJDB4992 | ENA
Project description:Large surface-to-volume ratios provide optimal nutrient uptake conditions for small microorganisms in oligotrophic habitats. The surface area can be increased with appendages. Here we describe chains of interconnecting vesicles protruding from cells of the flavobacterial strain Hel3_A1_48 originating from coastal free-living bacterioplankton. The chains were up to 10 µm long, had vesicles with a single membrane and a size of 80-100 nm by 50-80 nm, and emanated from the outer membrane. Cells extruded membrane tubes in the exponential phase, whereas vesicle chains dominated on cells in the stationary growth phase. This indicated a formation by pearling, which describes a physical morphogenic process: membrane tubes are protruding from liposomes and transform into chains of interconnected vesicles. Proteomes of whole cell membranes and of detached vesicles were dominated by outer membrane proteins including the type IX secretion system and surface-attached peptidases, glycoside hydrolases and endonucleases. Imported fluorescein-labeled laminarin was present in the periplasm of the cells and in the lumen of protruding vesicle chains. The appendages thus provide degradative enzymes on their surfaces and storage volume in the periplasmic extension, which seems to contribute to the high abundance of the Formosa-affiliated bacteria during laminarin utilization shortly after algal blooms.
2019-07-25 | PXD012522 | Pride