Depth structures metabolic potential and warming responses in marine microbial eukaryotes

Microbial eukaryotes are key drivers of food-web dynamics and nutrient cycling across the ocean's water column. Yet, how their metabolic potential is structured through depth remains largely unknown, limiting our ability to understand how microbial communities mediate biogeochemical transformations and how these functions may shift under climate change. Here, we combined a global-scale metagenomic analysis of tropical and subtropical samples spanning the full water column with bathypelagic metatranscriptomics to identify depth-dependent functional patterns across plankton size fractions. At depth, the functional composition of the nanoplankton size fraction was consistent with the export of surface-derived biomass, whereas the picoplankton size fraction showed signatures of resident communities, including depth-specific heterotrophic functions and bathypelagic-restricted fungal assemblages. Metabolic functional diversity was tightly coupled to taxonomic composition along the water column. Heterotrophic lineages contributed to phosphorus and sulfur acquisition at depth, revealing an undercharacterised eukaryotic role in deep-ocean nutrient cycling. Projections under end-of-century warming revealed spatially structured metabolic responses: subtropical intensification of photosynthetic capacity, subpolar stimulation of aerobic metabolism, and a decline of heterotrophic potential consistent with metabolic rebalancing within mixotrophic taxa. Our findings highlight the importance of marine microbial eukaryotes in ocean biogeochemistry, reveal their distinct functional roles across depths, and provide novel projections of how their metabolic potential may change under ocean warming.