Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA16339 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:North Pacific Subtropical Gyre Microbial Community
| PRJNA394135 | ENA
Project description:Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world’s oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
2013-03-07 | GSE44448 | GEO
Project description:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
2013-03-07 | E-GEOD-44448 | biostudies-arrayexpress
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.
2018-09-03 | GSE109218 | GEO
Project description:North Pacific Subtropical Gyre diel marine metatranscriptomes
| PRJNA437978 | ENA
Project description:North Pacific Subtropical Gyre eukaryotic plankton metatranscriptome sequencing
| PRJNA278441 | ENA
Project description:Community transcriptome from the North Pacific Subtropical Gyre
| PRJNA33463 | ENA
Project description:Microbial Metatranscriptome from Lagrangian time series in North Pacific Subtropical Gyre
| PRJNA244754 | ENA
Project description:Dataset from a shipboard incubation experiment of an ocean surface-water microbial community sampled at 25m depth at Station ALOHA in the North Pacific Subtropical Gyre. Incubations were amended with ammonium, glutamate, leucine, nitrate and urea, in two isotopic variants: 15N (to track incorporation by various community members) and 14N (for quantitation of abundance changes by diDO-IPTL).
2022-03-23 | MSV000089118 | MassIVE