Marine environmental water samples in the Eastern Tropical Pacific Ocean
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA983277 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Eastern Tropical North Pacific metagenome Raw sequence reads
| PRJNA1124864 | ENA
Project description:Eastern Tropical North Pacific Seawater Raw sequence reads
| PRJNA863324 | ENA
Project description:Untargeted proteomics from a 5,000 km+ transect across the central Pacific Ocean from Hawaii to Tahiti. The expedition crossed multiple biogeochemical provinces, inlcuding the oligotrophic North Pacific Subtropical Gyre, the extremety of the Eastern Tropical North Pacific Oxygen Deficient Zone, and the relatively productive equatorial region associated with upwelling. This dataset focuses on the microbial fraction (0.2-3.0 micrometer filter size) and the microbial community dynamics across these biogeochemical provinces, from the surface oceance to the mesopelagic (1,250 m depth maximum).
2022-08-31 | PXD030684 | Pride
Project description:Peptides and proteins were identified using a novel de novo-discovery approach in suspended and sinking organic particles from the eastern tropical North Pacific and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. De novo peptide sequencing, where the sequence of amino acids is determined directly from mass spectra rather than from comparison to theoretical spectra from a selected sequence database, was found to be a useful tool for discovery of peptides present in a sample but not initially included in the search database. Iterative de novo-informed database search results suggested the presence of fungal peptides and proteins in deep sinking particles, consistent with growing evidence that fungi play an important role in degradation of sinking material in the ocean. The de novo-discovery approach also allowed the tracking of modified autotrophic cyanobacterial peptides to the deep sea, where they contributed 0.63% of the phylum-level identifiable peptide pool in a bathymetric sediment trap sample. Overall, the amino acid composition of the peptides in the sinking material showed little change with depth, consistent with earlier observations of bulk organic matter and/or amino acid composition during the early stages of degradation. However, we identified an abundance of modified amino acids in sinking and suspended particles, including high levels of deamidation, suggesting that partial degradation of protein could potentially fuel observed anammox and contribute to observed pool of refractory organic nitrogen. We also observe methylation of arginine, which has previously been shown to slow degradation of peptides in seawater. Our results demonstrate several examples how de novo-discovery allows for a deeper evaluation of proteins and peptides in environmental systems undergoing degradation.
2022-01-10 | PXD023187 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE22171: Pacific salmon gill samples: fate tracking in river, sampled in ocean GSE22177: Pacific salmon gill samples: fate tracking in river GSE22347: Pacific salmon gill samples: fate tracking at spawning grounds Refer to individual Series
2010-12-31 | E-GEOD-22179 | biostudies-arrayexpress
Project description:The diazotroph Trichodesmium is an important contributor to marine dinitrogen (N2) fixation, supplying so-called new N to phytoplankton in typically N-limited ocean regions. Identifying how iron (Fe) and phosphorus (P) influence Trichodesmium activity and biogeography is an ongoing area of study, where predicting patterns of resource stress is complicated in part by the uncertain bioavailability of organically complexed Fe and P. Here, a comparison of 26 metaproteomes from picked Trichodesmium colonies identified significantly different patterns between three ocean regions: the western tropical South Pacific, the western North Atlantic, and the North Pacific Subtropical Gyre. Trichodesmium metaproteomes across these regions significantly differed in KEGG submodule signals, and vector fitting showed that dissolved Fe, phosphate, and temperature significantly correlated with regional proteome patterns. Populations in the western tropical South Pacific appeared to modulate their proteomes in response to both Fe and P stress, including a comparatively low relative abundance of the N2 fixation marker protein, NifH. Significant increases in the relative abundance of both Fe and P stress marker proteins previously validated in culture studies suggested that Trichodesmium populations in the western North Atlantic and North Pacific were P-stressed and Fe-stressed, respectively. These patterns recapitulate established regional serial and co-limitation patterns of resource stress on phytoplankton communities. Evaluating community stress patterns may therefore predict resource controls on diazotroph biogeography. These data highlight how Trichodesmium modulates its metabolism in the field and provide an opportunity to more accurately constrain controls on Trichodesmium biogeography and N2 fixation.
2025-06-17 | PXD057942 | Pride
Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series is of gill expression profiles from the study of fish sampled and tagged in the ocean and tracked as they entered the river system and swam towards the spawning grounds.
2010-12-31 | GSE22171 | GEO
Project description:Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
2019-02-12 | PXD009712 | Pride
Project description:Analysis of population structure and connectivity of Octopus mimus in the Eastern Pacific
| PRJEB34803 | ENA
Project description:Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub?Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
2021-11-05 | MSV000088323 | MassIVE