The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition.