Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

吞噬作用是海洋生态系统中的一个基本过程，通过该过程消耗猎物生物并将其生物量纳入食物网或再矿化。然而，在自由生活的吞噬原生生物中寻找这一关键生态过程背后基因的研究仍然很少，部分原因是缺乏适当的生态模型。我们对最近分子数据集的重新分析表明，培养的异养鞭毛虫Cafeteria burkhardae在全球海洋中广泛存在，这促使我们设计了一项针对该物种的转录组学研究，该物种与培养的黄杆菌Dokdonia sp 一起生长。我们比较了指数期和稳定期之间的基因表达，其中以中间状态出现的三个稀释期饥饿来补充。我们在每种条件下发现了不同的表达谱，并在指数样本和稳态样本之间鉴定了 2056 个差异表达基因。指数期上调的基因与DNA复制、转录和翻译机制、蛋白质重塑、呼吸和吞噬作用有关，而稳定期上调的基因涉及信号转导、细胞粘附和脂质代谢。我们鉴定了一些高表达的吞噬基因，如肽酶和质子泵，可用于针对海洋生态系统中的这一生态相关过程。