Deciphering the deep-sea ecosystem biodiversity: insights into its complexity using genomic approaches

The deep-sea is recognized as the largest ecosystem on Earth, and an extreme environment. The deep-sea normally refers to oceans with depth greater than 200 m, with about 50% of the surface of the Earth covered by ocean deeper than 3,000 m. The deep-sea ecosystem is characterized by low temperatures (usually <4°C, though fluids emitted at hydrothermal vents may reach 450°), high hydrostatic pressure, absence of sunlight, restricted primary production, and limited food availability. Despite these extreme conditions, living species can be found throughout the water column and in all seabed ecosystems to 11,000 meters in depth. Only 5% of the deep oceans have been thoroughly explored to date, and less than 0.001% described. Thus, the main aim of this thesis is to shed some lights on deep-sea ecosystem, through different genomic approaches. Indeed, the first chapter describes the steps to reach a "reference" genome of an organism that lives in and is well adapted to this ecosystem (the meso- bathypelagic fish Chauliodus sloani, belonging to Stomiiformes order). In the second chapter, we aim to evaluate fungal and microeukaryotic diversity of deep-sea sediments from Pacific and North Atlantic Oceans through a metabarcoding approach. The third and last chapter aims to describe the viral diversity in deep-sea sediments from North Atlantic Ocean using a viral metagenomic approach. These studies will expand our knowledge on the species and on the biodiversity of this ecosystem and will increase the reported data.