Marine plankton diversity across in situ observation types, assembling methods, and seasons.

Marine plankton are incredibly diverse and play a central role in regulating ocean ecosystems. They drive primary production, sustain higher trophic levels, and export anthropogenic carbon to the deep ocean. Yet, different in situ observation types and diversity metrics capture distinct ecological processes, and the quantitative links between plankton diversity and ecosystem functioning remain only partially understood. Here, we use a state-of-the-art habitat modeling framework (CEPHALOPOD) to provide a unified assessment of global plankton diversity across occurrence, abundance, biomass and metagenomic observations. Our analysis is based on the regression output of more than 330,000 species-level in situ observations against environmental climatologies, enabling a scale-consistent comparison across data types, diversity assembling methods, and seasons.

We show that a pronounced latitudinal diversity gradient emerges across all estimates, but important divergences occur in high latitudes and coastal upwelling systems. Qualitative diversity estimates such as those constructed from occurrences and species richness, highlight productive or heterogeneous environments where many taxa co-occur despite strong bloom dynamics. By contrast, quantitative diversity estimates based on abundances, biomass, or metagenomic reads provide a complementary view linked to community evenness and persistent environmental stability, particularly within tropical oligotrophic gyres. Variance partitioning further reveals that these differences arise from distinct environmental drivers: productivity predominantly shapes occurrence-based diversity, whereas carbonate chemistry and temperature more strongly influence quantitative and metagenomic diversity.

Finally, we demonstrate that plankton diversity patterns, across all axes of variance considered, serve as robust indicators of key ecosystem properties. Qualitative diversity closely tracks global net primary production, reflecting its sensitivity to productivity-driven species turnover. In contrast, quantitative and metagenomic diversity correlate strongly with carbon export efficiency, consistent with their ecological link community evenness and trophic transfer. All diversity estimates also correlate with global megafauna diversity, revealing a coherent structuring of marine communities from microbes to upper trophic levels. Overall, this diversity intercomparison unifies complementary perspectives on plankton community structure and ecosystem functioning, providing a scalable framework to quantify the drivers of marine biodiversity globally.