Taxonomic composition and ecophysiology of resident bacteria associated with marine phytoplankton

Dinoflagellates and diatoms are key marine phytoplankton, with ecological roles strongly influenced by their associated phycosphere bacteria. However, the ecophysiological functions of these bacteria remain enigmatic as a result of insufficient taxonomic and genomic characterization. Here, by combining single-cell isolation with a custom statistical pipeline, we profiled resident bacterial communities associated with 108 diatom and 86 dinoflagellate strains, collected across temperate and tropical oceans worldwide. We examined genomic traits of key bacterial populations through whole-genome sequencing of representative isolates. Taxonomic compositions of dinoflagellate- and diatom-associated microbiota were distinct, highlighting host-specific differences. Each microbiota harboured characteristic genera with adaptive traits reflecting host metabolic profiles. Dinoflagellate-associated bacteria were enriched in genes responsible for motility and sulfur-compound use, whereas diatom-associated bacteria specialized in glycan use. We identified 'foundation' genera, defined as taxa with high occupancy and community-level impact in both phycosphere types (for example, Marivita and Marinobacter), sharing host-specific traits with characteristic bacteria while universally excelling in environmental response and resistance. Notably, foundation bacteria were enriched in Type VI secretion systems, emerging as a universal hallmark of phycosphere bacteria across global oceans. Overall, this study provides insights into the taxonomic and metabolic nature of phycosphere bacteria, highlighting the profound influences of interspecific interactions on marine ecological processes.