Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Environmental molecular sequencing has revealed an abundance of microorganisms that were previously unknown, mainly because most had not been cultured in the laboratory. Within this novel diversity there are the uncultured MAST clades (MArine STramenopiles), which are major components of marine heterotrophic flagellates thought to be active bacterial grazers. In this study, we investigated the gene expression of natural heterotrophic flagellates in a mixed community where bacterivory was promoted. Using FISH (Fluorescence in situ hybridization) and 18S rDNA metatranscriptomics, we followed the taxonomic dynamics during the incubation, and confirmed the increase of the relative abundance in different MAST lineages. We then used single cell genomes of several MAST species to gain an insight into the most expressed genes related to phagocytosis. Most of the transcripts were assigned to both, subclade MAST-4A and -4B where we identified highly expressed genes involved in motility and cytoskeleton remodeling, as well as active lysosomal enzymes. Particularly relevant were the cathepsins, which are characteristic of the acidified phagolysosome. The combination of single cell genomics and metatranscriptomics provides a quantitative measure of the presence and prevalence of uncultured heterotrophic flagellate species along with its ongoing phagocytic capacity.