Abstract

This study presents the distribution of phytoplankton assemblages throughout cross-shelf and latitudinal gradients in the Chilean Patagonia along the Cape Horn Current System. High-resolution spatial surface data (every similar to 5 km) was collected during five oceanographic cruises conducted between 2018 and 2024, during the austral spring or summer, across latitudes 41 degrees S to 54 degrees S, spanning areas from the continental shelf to inner channels and fjords. Continuous underway phytoplankton measurements were obtained along vessel tracks using an Imaging FlowCytobot (IFCB), along with concurrent temperature and salinity measurements obtained using an Ocean-PackTM CUBE observation platform. We used the Outlying Mean Index (OMI) combined with niche overlap analysis to identify eight phytoplankton groups sharing ecological preferences. These groups exhibited varying affinity to different environmental conditions associated with the distinct water masses in Chilean Patagonia. This reflects the dynamic interplay between hydrography and community structure throughout the cross-shelf gradient in Chilean Patagonia. These results suggest that connectivity between inner seas and the continental shelf plays a critical role in determining the cross-shelf distribution of phytoplankton assemblages and harmful algal blooms (HAB) dynamics.