Overturning circulation structures the microbial functional seascape of the South Pacific.

Global overturning circulation partitions the deep ocean into regions, each with different physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems remains unknown. In this work, we integrate extensive genomic information with hydrography and water mass age to delineate microbial taxonomic and functional boundaries across the South Pacific. Prokaryotic richness steeply increases with depth in the surface ocean, which forms a so-called phylocline, below which, richness is consistently high, dipping slightly in highly aged water. Reconstructed genomes self-organize into six spatially distinct taxonomic cohorts and 10 functionally distinct biomes that are primarily structured by wind-driven circulation at the surface and density-driven circulation at depth. Overall, water physicochemistry, modulated at depth by water age, drives microbial diversity patterns and functional potential in the pelagic ocean.