Invisible to the naked eye, planktonic prokaryotes—comprising both bacteria and archaea—represent a large fraction of marine biomass, with abundances typically ranging from thousands to millions of cells per millilitre. From primary producers (photo- and chemoautotrophic) to heterotrophs, they display extremely diverse metabolisms and are of the utmost importance for the biogeochemical cycles in the ocean. During their involvement in elemental cycling, prokaryotes interact with the organic matter continuum (particulate and dissolved), utilising it as source of energy and carbon. In doing so, they transform the organic matter pool, diversifying it and remineralising compounds into their inorganic constituents. Moreover, by converting organic matter into biomass, prokaryotes return carbon into the marine trophic webs, a process known as the microbial loop. Hence, this pathway is crucial for organic matter cycling in the oceans. Upwelling regions represent some of the most productive marine systems, with large pools of organic matter subject to dynamic interactions with prokaryotic communities. Such environments thus have major importance for carbon cycling at the global scale, making very relevant the study of the prokaryotes that inhabit them. In this thesis we combine mesocosm experiments and synoptic field samplings to study prokaryotic communities in upwelling environments, with special attention to how they relate to organic matter cycling. The first half of the thesis is devoted to an upwelling simulation experiment carried out in the oligotrophic waters of the subtropical Eastern North Atlantic. By simulating different upwelling intensities and frequencies (singular pulse versus recurring upwelling), we studied how the dissolved organic matter pool and the prokaryotic communities respond to variable upwelling scenarios. First, we measured the dissolved organic matter concentrations and optical properties, observing that upwelling intensity was positively related to dissolved organic matter accumulations. Singular and recurring upwellings yielded mostly similar changes in concentrations and optical properties despite the markedly contrasting outcome of their phytoplankton blooms (a single large bloom in the singular mode versus sustained smaller blooms in the recurring one). Although optical properties suggested ongoing transformation of organic matter, the accumulated dissolved organic matter did not decrease, indicating that during the experiment production and consumption tended to be balanced. In parallel, prokaryotic successional patterns also displayed remarkable similarities in singular and recurring upwelling treatments. The dominant taxa within the successional assemblages differed mostly between the particleassociated and the free-living fractions, but upwelling modes also displayed some differences in composition. Thus, it is striking that prokaryotic communities shared common successional patterns even across size fractions under the different blooming scenarios. The second half of the thesis in turn explores how the influence of upwelling propagates down in the water column, addressing the vertical connectivity between highly productive surface waters and the prokaryotic communities inhabiting the water masses of the dark ocean. We studied natural communities along an oceanographic transect in the tropical and subtropical Atlantic (which included areas under the influence of the Northwest African upwelling system), showing how the standing stocks and physiological status of meso- and bathypelagic prokaryotes are coupled with surface productivity. We showed that the cell-viability of deep ocean prokaryotes increased under the productive waters of the upwelling, evidencing that its effect reaches the deep layers. The analysis of the water masses also showed that the distribution of prokaryotic taxa and the optical properties of dissolved organic matter were explained in varying degrees by i) the mixing and ageing history of water masses, and ii) intraregional biogeochemical processes (including links to surface productivity). Thus, we conclude that upwelling markedly influences the dissolved organic matter and prokaryotic communities of surface and deep waters