Abstract
During a spring‐summer bloom in a large Arctic polynya, vertically distinct protist communities (phytoplankton and protozoa) occurred within layers caused by interleaving and entrainment of different water masses. We developed a ternary community distance index to quantify the variability in protist community structure in these heterogeneous surface layers. This index was highly correlated ( r = 0.984, n = 6) with the extent of physical interleaving (quantified as the root mean square deviations in temperature between measured and smoothed profiles) indicating a high degree of physical‐biotic coupling within water columns of the polynya. Water mass layering created favorable conditions for ciliate blooms. These blooms were associated with distinct temperature‐salinity layers. These layers might act as processing traps for particulate organic matter, with highest concentrations of viruses and bacteria (specifically cells with open or leaky membranes, suggesting microbial grazing pressure) occurring in highly interleaved water columns. In contrast, viral and bacterial concentrations were lowest at a noninterleaved station where protist biomass was dominated by flagellates and small dinoflagellates that were evenly distributed down the water column. Water mass interleaving is likely to contribute to microbial biodiversity, community structure and vertical segmentation of biogeochemical processes in the upper ocean.