This project consists of analyses of of planktonic microbial communities in a region of the North Pacific Ocean.
More...This project consists of analyses of of planktonic microbial communities in a region of the North Pacific Ocean. The Subtropical Gyre consists of a clockwise swirling vortex of ocean currents that make up most of the northern Pacific Ocean. Samples were taken at different depths (10 m to 4000 m) at the Hawaii open-ocean time-series station ALOHA (22
o45' N, 158
oW) and large DNA fragments were cloned (36 kbp fosmids) from the samples and shotgun sequenced. A comparison of protein sequences encoded by samples at various depths and clustering of functional categories revealed definite gradients. For example, proteins involved in photosynthesis were found in the photic zone, as expected, while proteins involved in surface attachment were more prevalent in deep samples, suggesting a greater tendency for surface colonization at those ocean depths.
There are a set of GenBank Accession Numbers associated with this study. DU731018-DU796676 and DU800850-DU800864 correspond to fosmid end sequences while DQ300508-DQ300926 are the small subunit ribosomal RNA sequences.
In addition EF089401-EF089402 , EF100190-EF100191 , EF107101-EF107103 , EF107106 , EU016559-EU016674 and GQ412706-GQ412710
are genomic sequences derived from this study.
454 sequence data is available from the Short Read Archive (SRA): SRA000262 and SRA000263.
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Project Data Type: Metagenome, Genome sequencing, Targeted Locus (Loci); Locus Tag Prefix:ALOHA
Attributes:Scope: Environment; Material: Genome; Capture: Whole; Method type: Sequencing
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| Nucleotide (total) | 552 |
| WGS master | 1 |
| Genomic DNA | 551 |
| SRA Experiments | 14 |
| Capillary Traces (Trace Archive) | 1 |
| Protein Sequences | 5057 |
| Publications |
| PubMed | 4 |
| PMC | 2 |
| Other datasets |
| BioSample | 15 |
| GSS | 65674 |
| PopSet | 1 |
Publications:
- Martinez A et al., "Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses.", Environ Microbiol, 2009 Sep 29;12(1):222-38
More...
- Martinez A et al., "Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses.", Environ Microbiol, 2009 Sep 29;12(1):222-38
- Konstantinidis KT et al., "Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre.", Appl Environ Microbiol, 2009 Jun 19;75(16):5345-55
- Frias-Lopez J et al., "Microbial community gene expression in ocean surface waters.", Proc Natl Acad Sci U S A, 2008 Mar 3;105(10):3805-10
- DeLong EF et al., "Community genomics among stratified microbial assemblages in the ocean's interior.", Science, 2006 Jan 27;311(5760):496-503
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[Taxonomy ID: 408172] Submission:
Registration date: 18-Jul-2007
DOE Joint Genome Institute