We knew that the rates of many cellular processes change with temperature, so we hoped we could use transcriptomics to identify common physiological mechanisms used by diatoms to respond temperatures above and below their optimal growth temperature.
Julie Koester and Yue Liang were the perfect team for this project. Julie had worked with diatoms as a graduate student at the University of Maine and then the University of Washington. Julie selected two strains of Chaetoceros affinis, one isolated from cold waters off the coast of Nova Scotia (Canada) and the other from warmer waters near the coast of Marseilles (France). She grew the two strains at a range of temperatures to characterize their thermal performance curve and collected samples for transcriptomic analyses at their optimal growth for temperature and a cooler sub-optimal and warmer supra-optimal growth temperature for their growth. Yue had bioinformatic experience from her work at Tokyo University of Agriculture and Technology working on the oil-rich diatom Fistulifera solaris. With her knowledge of biochemistry, physiology, and metabolism, we were able to untangle the transcriptomic response of diatoms to temperature.
Our plan was to see how an increase and decrease in growth temperature relative to each species’ optimum for growth affected gene expression in balanced growth. Of course we hoped the two species would act as replicates–we would see largely the same pattern in each species. It didn’t work out quite that simply! It turns out that, even in two closely related diatoms with only a few degrees separating their optimal temperatures, there are a lot of differences in the transcriptome with changes of only 5°C. When we first looked at the results, we despaired – there didn’t seem to be any general patterns!
Ultimately it was similar work in corals that gave us the inspiration to untangle the patterns in the transcriptomes. In corals, adaptation to higher temperatures has been shown to permanently shift base-line expression of some genes, in a phenomenon known as front-loading, to prepare corals for further changes in temperature. In our diatoms, we noticed that the diatom adapted to warmer conditions often didn’t differentially express genes under elevated supra-optimal growth temperatures. We inferred this was a result of adaptive increases or decreases in gene expression, which we call investment or divestment. Through this lens, a complicated array of transcriptome changes became like a complex puzzle with interlocking pieces that fit together. While fundamental physiology determines the pathways and mechanisms of temperature acclimation, evolutionary history strongly influences the responses of even closely related species to environmental change. There are, naturally, a few holes and a few left-over puzzle pieces, but we were thrilled that an insight from corals combined with established biochemistry could help us assemble a complex puzzle of interactions and changes.