Return of the marine heterotrophic flagellates: diversity, distribution and gene expression patterns

Abstract

Marine heterotrophic flagellates (HF) are very small (2-5 μm) unpigmented protists that are dominant bacterial grazers in the ocean, where they link the transfer of carbon from bacterial cells to higher trophic levels. Through their bacterivorous activity, they also act as nutrient recyclers that allow for regenerated primary production, and they are partially responsible of keeping bacterial abundances in the ocean fairly constant. HFs are widespread throughout the eukaryotic tree of life, ubiquitous in the plankton and display a high functional diversity. During the last decades of the twentieth century, a growing interest in this functional group occurred, and studies were performed to characterize their ecological role. However, this initial attention diminished due to the difficulty to study natural HF species, as they possess few morphological traits for identification and generally remain uncultured. Consequently, HFs have been often neglected in marine surveys, to the extent of becoming one of the most understudied components of the marine microbiome. With the advent of high-throughput sequencing and the reduction of sequencing costs, studying these protists at a high-resolution level became feasible. This thesis represents a return to the study of HFs using these newly developed tools. We first investigated the distribution patterns of eukaryotic diversity along the water column of the ocean by metagenomics and compared the results with metabarcoding approaches. This analysis revealed a clear separation of taxonomic groups between pico- (0.2-3 μm) and nanoplanktonic (3-20 μm) fractions, as well as between photic (0-200 m) and aphotic (>200 m) regions. While some groups were not well represented by metabarcoding approaches due to technical biases, HFs were generally not affected by them. We then studied the diversity and distribution of HFs in the ocean using global metabarcoding data sets. With this, we identified a few dozens of HF species, most of them uncultured, as the dominant in surface and deep ocean regions. Many of these dominant species were present at relatively constant abundances, while others were influenced by temperature or displayed patchy distributions. Finally, we jumped from global patterns to study the gene expression of HFs in natural assemblages growing by bacterivory in unamended incubations. The obtained results using metatranscriptomics sequencing showed similar functional dynamics between experiments done at different times of a seasonal cycle, with marked differences between incubation times. Genes related to cysteine peptidases as well as some glycoside hydrolases emerged as key components involved in the process of bacterivory. Overall, this thesis returns HFs back to the spotlight and creates a solid foundation on which to perform renewed research on the ecology and functional role of this group