By tracking the water mass histories of genetic samples, we investigated the biophysical dynamics shaping eukaryotic phytoplankton populations in a nutrient-deplete subtropical gyre, where cyanobacteria have a competitive advantage. Triplicate seawater samples were filtered every [Formula: see text]46 km along a 2,382 km North Pacific transect, spiked with genomic internal standards, and amplified with a three-domain primer set to obtain absolute 16S and 18S rRNA volumetric gene abundances. The transport histories of each sample were simulated by advecting mesoscale Lagrangian particle clouds in satellite remote sensing velocity fields. Consistent with previous field studies, eukaryotic phytoplankton were anomalously abundant within eddies and along eddy-edges, where vertical circulations redistribute nutrients. Outside of eddies, we found a statistically significant decline in eukaryotes as a function of lateral coherence: Waters that recently mixed from multiple origins supported eukaryote anomalies resembling those of eddies, whereas eukaryotic populations were depressed from isolation in waters that were coherent for three or more months. In these coherent outside-eddy water masses, we estimate taxon-dependent eukaryote population half-lives range from 8 to 17 mo. Such physical conditions are relatively rare, given that [Formula: see text]90% of the entire gyre during the sampling campaign was composed of eddies and recently mixed waters. These results derived from empirical observations substantiate the theory that eukaryotic phytoplankton would face exclusion in the subtropics on timescales of [Formula: see text]years due to competitive pressure from cyanobacteria, yet are sustained in small numbers by regular disturbances promoting opportunistic growth and dispersal.
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