Microorganisms in the ocean conform an extensive microbiome where individuals interact constantly with the particulate matter. However, most of the studies have focused on the free-living microorganisms, and to a lesser extent on the attached microorganisms but have not taken into account the organisms associated to particles of different sizes. The main objective of this thesis is to characterize the diversity of prokaryotes along the particulate matter continuum present in the ocean, as well as to describe its temporal and spatial variability at distinct scales. First of all, we propose a multiple size-fractionation as a sampling method that provides a better comprehension of the prokaryotic diversity than the commonly used sampling methods. Our work shows that each size-fraction contains distinct prokaryotic communities that vary at different spatial and temporal scales. In general, there is an increase of bacterial richness from the smaller to the larger particles, suggesting that larger particles may contribute with new niches. The main exception is the bathypelagic, where richness decreases form the small to the largest size-fractions. In contrast, Archaea presented higher richness in the smaller size-fractions and, although had lower diversity and relative abundance than bacteria, these increased with depth. We moreover classified taxonomic groups depending on whether they have preference for small size-fractions, for larger size-fractions, or do not have a clear preference for any size fraction. This classification is presented as an alternative to the traditional simple separation between free-living bacteria and attached bacteria. Most of the taxonomic groups maintain their preference for certain size fractions in space and time, although some taxonomic groups change their preferences in vertical profiles from the surface to the bathypelagic and along time. We also observed that the bathypelagic is dominated by prokaryotes which are also present in surface waters and that there is a vertical connectivity between prokaryotic communities along the water column through sinking particles. This connectivity causes bathypelagic biogeography to be closely linked to particle colonization in the ocean surface. Overall, this thesis reports on the complexity of prokaryotic communities present in the continuum of sizes and shows the need for disseminating this perspective to define more comprehensively the diversity of ocean prokaryotes