Phytoplankton community composition and gene expression of functional genes involved in carbon and nitrogen assimilation

Journal of Phycology

Volumn 44, Issue 6, 2008, Pages 1490-1503

  Ward, B B ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

Community composition; Diatoms; Gene expression; Microarray; Nitrate reductase; Phytoplankton; rbcL

Indexed keywords

BACILLARIOPHYTA; EUKARYOTA; HAPTOPHYCEAE; MASTIGOPHORA (FLAGELLATES); PHAEODACTYLUM TRICORNUTUM; UNCLASSIFIED CHLOROPHYTA;

EID: 52949112412     PISSN: 00223646     EISSN: 15298817     Source Type: Journal    
DOI: 10.1111/j.1529-8817.2008.00594.x     Document Type: Article

References (20)

1. Allen, A. E., Ward, B. B. Song, B. K. 2005. Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities. J. Phycol. 41 : 95 104.
2. Dandonneau, Y., Montel, Y., Blanchot, J., Giraudeau, J. Neveux, J. 2006. Temporal variability in phytoplankton pigments, picoplankton and coccolithophores along a transect through the North Atlantic and tropical southwestern Pacific. Deep-Sea Res. Part I Oceanogr. Res. Pap. 53 : 689 712.
3. De Martino, A., Meichenin, A., Shi, J., Pan, K. H. Bowler, C. 2007. Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions. J. Phycol. 43 : 992 1009.
4. Dudley, A. M., Aach, J., Steffen, M. A. Church, G. M. 2002. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. U. S. A. 99 : 7554 9.
5. Dugdale, R. C., Wilkerson, F. P. Morel, A. 1990. Realization of new production in coastal upwelling areas: a means to compare relative performance. Limnol. Oceanogr. 35 : 822 9.
6. Hansen, M. C., Tolker-Nielsen, G., Givskov, M. Molin, S. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26 : 141 9.
7. Holligan, P. M. Harbour, D. S. 1977. Vertical distribution and succession of phytoplankton in western English Channel in 1975 and 1976. J. Mar. Biol. Assoc. U. K. 57 : 1075 93.
8. Kanagawa, T. 2003. Bias and artifacts in multitemplate poymerase chain reactions (PCR). J. Biosci. Bioeng. 96 : 317 23.
9. Llewellyn, C. A., Fishwick, J. R. Blackford, J. C. 2005. Phytoplankton community assemblage in the English Channel: a comparison using chlorophyll a derived from HPLC-CHEMTAX and carbon derived from microscopy cell counts. J. Plankton Res. 27 : 103 19.
10. Mackey, M. D., Mackey, D. J., Higgins, H. W. Wright, S. W. 1996. CHEMTAX - a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton. Mar. Ecol. Prog. Ser. 144 : 265 83.
11. Pingree, R. D., Pugh, P. R., Holligan, P. M. Forster, G. R. 1975. Summer phytoplankton blooms and red tides along tidal fronts in approaches to English Channel. Nature 258 : 672 7.
12. Pozhitkov, A., Noble, P. A., Domazet-Loso, T., Nolte, A. W., Sonnenberg, R., Stehler, P., Geier, M. Tautz, D. 2006. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res. 34 : e66.
13. Ricard, M. 1987. Atlas du Phytoplankton Marin, Vol. 2. Diatomophycees. Centre Nationale de la Recherche Scientifique, Paris, 215 pp.
14. Sanguin, H., Herrera, A., Oer-Desfeux, C., Deschesne, A., Simonet, M., Navarro, E., Voel, T. M., Meonne-Loccoz, Y., Nesme, X. Grundmann, G. L. 2006. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ. Microbiol. 8 : 289 307.
15. Schuster, G., Lisitsky, I. Klaff, P. 1999. Polyadenylation and degradation of mRNA in the chloroplast. Plant Physiol. 120 : 937 44.
16. Smyth, G. K. Speed, T. 2003. Normalization of cDNA microarray data. Methods 31 : 265 73.
17. Taroncher-Oldenburg, G., Griner, E., Francis, C. A. Ward, B. B. 2003. Oligonucleotide microarray for the study of functional gene diversity of the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69 : 1159 71.
18. Ward, B. B., Eveillard, D., Jackson, G. A., Nelson, J. D., Voytek, M. A. Jackson, G. A. 2007. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environ. Microbiol. 9 : 2522 38.
19. Wawrik, B., Paul, J. H., Campbell, L., Griffin, D., Houchin, L., Fuentes-Ortega, A. Muller-Karger, F. 2003. Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico. Mar. Ecol. Prog. Ser. 251 : 87 101.
20. Wurmbach, E., Yuen, G. Sealfon, S. C. 2003. Focused microarray analysis. Methods Enzymol. 31 : 306 16.