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
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:Microbial eukaryotes from the Western Pacific Ocean
Project description:Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities.
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.
Project description:we characterized the microbial communities and proteomes of POC collected from the twilight zone at three contrasting sites in the northwest Pacific Ocean using a metaproteomic approach.Particle-attached bacteria, Alteromonadales, Rhodobacterales and Enterobacteriales, were the major remineralizers of POC in the twilight zone.
2021-03-24 | PXD014630 | Pride
Project description:microbial assemblages in the western subtropical Pacific Ocean
| PRJNA791001 | ENA
Project description:Microbial community diversity in the Western Pacific Ocean