Significance Circumstantial evidence indicates that especially deep-ocean heterotrophic microbes rely on particulate organic matter sinking through the oceanic water column and being solubilized to dissolved organic matter (DOM) prior to utilization rather than on direct uptake of the vast pool of DOM in the deep ocean. Comparative metaproteomics allowed us to elucidate the vertical distribution and abundance of microbially mediated transport processes and thus the uptake of solutes throughout the oceanic water column. Taken together, our data suggest that, while the phylogenetic composition of the microbial community is depth stratified, the composition and substrate specificities of transporters considered in this study are ubiquitous while their relative abundance changes with depth.