Surface ocean microbial communities are responsible for half of global net primary production and form the foundation of marine food webs. The structure and function of these marine microbial communities is shaped by a network of metabolite-mediated interactions. Monitoring microbial transcriptomic or proteomic expression are effective ways to identify the metabolites that are exchanged, the community members involved, and the nature of the interactions in question. Particularly valuable genes to monitor are transporters as they are the cell’s interface with its surroundings and the mechanism for obtaining extracellular metabolites. Expression-based approaches are limited, however, by the difficulty of accurately assigning functions to many genes, particularly in environmentally relevant microorganisms. In this dissertation I use experimental and computational approaches to characterize the function of genes mediating chemical exchanges in the model marine bacterium Ruegeria pomeroyi DSS-3, elucidating the role of metabolites in various interactions. Using an arrayed library of R. pomeroyi knockout mutants, I experimentally characterized 13 influx transporters of environmentally important metabolites. These included the transporters of citrate and 3-hydroxybutyrate, which were among the most highly expressed genes during a dinoflagellate bloom in Monterey Bay. The characterized ATP-binding cassette (ABC) transporters informed a phylogeny-based approach for cognate substrate identification, finding that the ATPase component of the multi-protein transporter most accurately and consistently identifies cognate substrates. This approach was applied to identify taurine transporters in global ocean metagenomes, revealing a strong signal of higher frequency in polar environments. Finally, I characterized a key gene in the biosynthesis pathway of indole-3-acetic acid (IAA), a phytohormone and interdomain signaling molecule. R. pomeroyi, though it lacks a complete biosynthesis pathway, can produce IAA when provided the precursor indole-3-acetamide (IAM). A two-way IAM-IAA exchange interaction occurs between R. pomeroyi and a diatom when cultured together. Interactions based on the exchange of IAM are common in nature as many environmental bacterial isolates have an incomplete IAA biosynthesis pathway similar to that of R. pomeroyi. Together these findings highlight the importance of metabolite transport and trade in microbial communities and demonstrate the value of functional gene annotation for understanding the mechanisms and ecology of microbial exchanges.