Using functional genomics to explore the effects of ocean acidification on calcifying marine organisms

As the research community attempts to forecast the effects of ocean acidification on marine ecosystems, a critical element is a clear understanding of the effects of ocean acidification on an individual organism's physiology. This article explores how the use of genomics-based tools that measure gene expression-DNA microarrays and quantitative PCR - can assist in this effort and reveal aspects of how calcifying marine organisms will respond to ocean acidification. More specifically, what stands to be gained from this approach is an understanding of the direct effects of ocean acidification and whether organisms have sufficient physiological plasticity to adapt to the altered CO2 conditions. We provide a brief overview of biomineralization processes in corals and sea urchin larvae, and then link these pathways to ways in which gene expression analysis can reveal physiological responses and mechanisms, and further, can define new testable hypotheses. In addition, we review the resources available and strategies that might be taken for each of 2 study organisms, stony corals and sea urchins. Finally, we suggest strategies for gene expression profiling in organisms that differ in availability of genomic resources.