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| Status |
Public on Sep 12, 2008 |
| Title |
Phytoplankton community composition and gene expression involved in carbon and nitrogen assimilation |
| Platform organisms |
Phaeodactylum tricornutum; Dunaliella tertiolecta; Chlamydomonas reinhardtii; Pseudochlorella pringsheimii; Asterionellopsis glacialis; Cylindrocystis sp. UTEX 1925; uncultured eukaryote; uncultured Chlorophyta; Haptophyta environmental samples |
| Sample organisms |
unidentified; uncultured organism |
| Experiment type |
Other
|
| Summary |
A functional gene microarray was developed and used to investigate phytoplankton community composition and gene expression in the English Channel. Genes encoding the CO2 fixation enzyme RuBisCO (rbcL) and the nitrate assimilation enzyme nitrate reductase (NR) representing several major groups of phytoplankton were included as oligonucleotide probes on the 'phytoarray'. Five major groups of eukaryotic phytoplankton that possess the Type 1D rbcL gene were detected, both in terms of presence (DNA) and activity (rbcL gene expression). Changes in relative signal intensity among the Type 1D rbcL probes indicated a shift from diatom dominance in the spring bloom to dominance by haptophytes and flagellates later in the summer. Because of the limitations of a smaller database, NR probes detected fewer groups, but due to the greater diversity among known NR sequences, NR probes provided higher phylogenetic resolution than did rbcL probes, and identified two uncultivated diatom phylotypes as the most abundant (DNA) and active (NR gene expression) in field samples. Unidentified chlorophytes and the diatom Phaeodactylum tricornutum were detected at both the DNA and cDNA (gene expression) levels. The reproducibility of the array was evaluated in several ways and future directions for further improvement of probe development and sensitivity are outlined. The phytoarray provides a relatively high resolution, high throughput approach to assessing phytoplankton community composition in marine environments.
Keywords: seawater natural assemblages, functional gene expression
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| Overall design |
Two functional genes, nitrate reductase and RuBisCO, 4 - 8 replicate features per array
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| Contributor(s) |
Ward BB |
| Citation |
B. B. Ward. Phytoplankton community composition and gene expression of functional genes involved in carbon and nitrogen assimilation (2008). Journal of Phycology, Vol 44 (6) 1490-1503. doi:10.1111/j.1529-8817.2008.00594.x.
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| |
| Submission date |
Sep 11, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Bess B Ward |
| E-mail(s) |
bbw@princeton.edu
|
| Phone |
6092585150
|
| Fax |
6092580796
|
| Organization name |
Princeton University
|
| Department |
Geosciences
|
| Lab |
Ward
|
| Street address |
Guyot Hall
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL7261 |
Princeton Biocomplexity Project, BC007 and BC008 |
|
| Samples (19)
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| Relations |
| BioProject |
PRJNA111035 |
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