Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Phagocytosis is very important in marine ecosystems and is one of the few purely eukaryotic processes with trophic relevance that can be addressed investigated by gene expression. These studies in free-living phagocytizing protists are scarce, in part due to the lack of useful ecological models. A recent protist diversity survey has unveiled that the cultured heterotrophic flagellate Cafeteria roenbergensis is widespread in the global ocean, and this prompted us to design a gene expression study with this species, grown in batch cultures with a cultured flavobacterium. We compared the gene expression between exponential and stationary phases, which were complemented with a starvation by dilution state that appeared between both phases. We showed contrasted functional expression profiles dynamics for each phase and pointed identified 1196 differentially expressed genes, 776 upregulated and 420 downregulated in the exponential phase. Genes highly expressed during the exponential phase were related to the translational machinery, protein remodeling, respiration and phagocytosis, while genes upregulated in the stationary phase were involved in lipid metabolism, cell signaling and cell adhesion.