This study integrates Tara Oceans meta-omics data to predict genome-scale interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network reveals significant inter-lineage associations across diverse phylogenetic distances. Co-active communities include species with smaller genomes but higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling highlights conserved metabolic cross-feedings, particularly of specific amino acids and group B vitamins. The integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may jointly shape bacterioplankton community assembly in the global ocean surface. The study provides insights into the functional self-organization of microbial communities and the mechanisms driving their assembly and activities.This study integrates Tara Oceans meta-omics data to predict genome-scale interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network reveals significant inter-lineage associations across diverse phylogenetic distances. Co-active communities include species with smaller genomes but higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling highlights conserved metabolic cross-feedings, particularly of specific amino acids and group B vitamins. The integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may jointly shape bacterioplankton community assembly in the global ocean surface. The study provides insights into the functional self-organization of microbial communities and the mechanisms driving their assembly and activities.