OLI Grant: Gene expression analysis to identify nutrient scavenging mechanisms in the coccolithophore Emiliania huxleyi

Sonya Dyhrman, Biology

Grant Funded: 2003

Proposed Research

Abstract
Coccolithophores are an abundant and widespread phytoplankton functional group responsible for significant amounts of calcification in the ocean. Although coral reefs are arguably the most visible example of marine calcification, the coccolithophore Emiliania huxleyi can form large (100,000km) blooms in both coastal and open ocean regions. These E. huxleyi blooms produce calcite that rains down onto the ocean floor in an important step in the global carbon (C) cycle. In short the presence of E. huxleyi blooms and the activities of the organisms within the population mediate exchange between atmospheric and oceanic CO 2 . Thus the distribution and activities of this species may have a significant impact on climate, and on the ocean?s ability to buffer changing CO 2 concentrations in the atmosphere. As such, there is considerable interest in the factors that influence these blooms, the physiology of the population therein, and the impact E. huxleyi blooms may have on the C cycle. In particular, we are interested in cellular nitrogen (N) and phosphorus (P) scavenging mechanisms. N and P availability likely impact when and where E. huxleyi blooms are able to occur, and N and P stress can influence CO 2 exchange by changing rates of photosynthesis and calcification.

With the upcoming availability of the E. huxleyi genome sequence (funded by the DOE Microbial Genomes Program, www.jgi.doe.gov) we are poised to make large advances in our understanding of E. huxleyi nutritional physiology and nutrient scavenging mechanisms. Here we propose a study to identify gene expression patterns associated with replete, N-stressed and P-stressed cells using long-serial analysis of gene expression (LongSAGE). Research identifying gene expression patterns associated with replete, N-stressed, and P-stressed cells, such as that proposed herein, will provide insight into how E. huxleyi obtains N and P. With an improved understanding of E. huxleyi N and P assimilation we can better identify how nutrient availability in the field may influence bloom dynamics, calcification and their concomitant impact on C cycling and global climate.

We anticipate this research to:

1. Specifically identify gene transcripts that are up or down-regulated in response to nutritional status in the globally significant coccolithophore Emiliania huxleyi .
2. Demonstrate the utility of LongSAGE analyses in the study of ocean biology and transfer the technological capability into the Dyhrman Laboratory.
3. Result in gene expression data that can be used for publication and as the basis for a proposal to NSF Biocomplexity (Genomics in the Environment) or Biological Oceanography.
4. Strengthen interactions between WHOI Biology and the MBL?s Josephine Bay Paul Center for Comparative Molecular Biology and Evolution.
   

Institute themes

The proposed work relates to the three Institute themes of

1) Biodiversity, 2) Health of Marine Ecosystems, and 3) New tools for Ocean Biology. Characterization of gene expression patterns will improve our understanding of how E. huxleyi interacts with its environment. The novel application of LongSAGE to E. huxleyi will identify target gene transcripts that may be indicative of N and P limitation, and will result in a new tool for the study of ocean biology. Probing for these targets in the environment would allow us to look at the relationships between nutrient availability, bloom formation, and calcification in situ . This is significant to ecosystem health because the activities of E. huxleyi and other calcifying marine organisms play an important role in mediating global climate. In summary, studies of E. huxleyi genomics such as that proposed here, will help us better predict the extent to which the marine C cycle will be influenced by increasing atmospheric CO 2.

Progress Report

Emiliania huxleyi, an abundant and widespread marine coccolithophore can form large blooms in both coastal and open ocean regions. Capable of forming calcareous skeletons and generating a steady rain of calcium carbonate to the deep sea, E. huxleyi plays a role in regulating the global carbon (C) cycle and ocean-atmospheric CO2 exchange that could have a significant impact on climate. Consequently, understanding the factors that influence E. huxleyi blooms and physiology are important. Specifically, we are interested in cellular nitrogen (N) and phosphorus (P) scavenging mechanisms as well as the response of cells to increased atmospheric CO2. N and P availability likely impact when and where E. huxleyi blooms are able to occur. N and P stress and enhanced CO2 may influence CO2 exchange by changing rates of photosynthesis and calcium carbonate production.

This project focuses on identifying gene expression patterns associated with nutrient replete, N and P deplete, and enhanced CO2 cells using Serial Analysis of Gene Expression (SAGE). To date, we have succeeded in obtaining a SAGE library for each of the different growth conditions. These libraries consist of roughly 15,000 tags, or nucleotide sequences, which correspond to the genes expressed within the cells. We have recently acquired access to a database that will help us identify the function of each of these sequences. Louie Wurch, a 2004 Summer Student Fellow, will be instrumental in this portion of the project.

Identifying gene expression patterns associated with different nutrient conditions and increased CO2 will help us identify how nutrient availability and changes in atmospheric CO2 in the field may influence bloom dynamics, calcification and their concomitant impact on carbon cycling and global climate.