Surface currents shape protist community structure across the Indo‐Pacific.

Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High‐throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo‐Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo‐Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top‐down pressures, such as grazing from higher trophic levels. [ABSTRACT FROM AUTHOR]