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The Transcriptome Response of Chaetoceros socialis during Moderate Silica Limitation
AuthorRead, Robert W.
AdvisorGrzymski, Joseph J.
Biochemistry and Molecular Biology
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Diatoms are ubiquitous microorganisms important in the global carbon cycle, because of their significant primary productivity. These phytoplankton require the nutrient silica to form their outer cell wall, however, surface concentrations of Si(OH)4, can be a limiting resource in oceanic regions, such as the Southern Ocean. Therefore, it is essential to identify how these microorganisms react to reduced silica concentrations. Here I report transcriptome sequencing results for the ubiquitous diatom Chaetoceros socialis in response to silica limitation. Using short paired-end sequencing, 92015 transcripts were assembled that were homologous to 6129 genes in the fully sequenced diatom Thalassiosira pseudonana. Silica concentrations in this experiment did not alter growth rate until day 5 and samples for differential gene expression were taken on day 2 when the growth rates of the two cultures were similar, and on day 5 when the growth rates of the cultures were different. Of the 92015 transcripts, there were 2238 transcripts corresponding to 344 homologous T. pseudonana genes (p-value 0.01) that showed a log2 fold change of greater than two in the silica stressed cultures compared to the silica replete cultures. Furthermore, there were 1758 transcripts corresponding to 100 homologous T. pseudonana genes that showed a log2 fold change of greater than two in the silica replete cultures compared to the stressed cultures, indicating an early response to silica stress. Differential expression analysis indicated genes associated with the pathways of glycolysis, the TCA cycle, and oxidative phosphorylation were all up-regulated in the reduced silica cultures compared to silica replete cultures. In the stressed cultures, transcripts in fatty acid biosynthesis were up-regulated, while transcripts in B-oxidation were down-regulated, suggesting that lipid content in the diatom may increase under silica limited conditions. Silica transporter transcripts also showed significant log2 changes, consistent with previous work. These data suggest that silica stress causes the cell to increase the concentration of high energy lipids, increase the concentration of ATP in order to carry out unfavorable reactions, such as fatty acid biosynthesis, and repurpose carbohydrate carbon skeletons into higher energy lipids. The up-regulation of silica transporter transcripts in the silica stressed cells showed there are fundamental differences in the diatom cell, as the organism transitions from internal silica regulation to extracellular silica regulation, even though growth rate does not change. These results demonstrate that C. socialis has developed an early, robust cellular response to silica limitation, which affects several different biochemical pathways within the cells, and may have implications for tuning diatoms to being better producers of biofuels