Deciphering patterns of protistan taxa is a crucial step for understanding anthropogenic and environmental impacts on biogeography. We characterized and compared protistan communities from environmental samples collected along a major shipping corridor, the Panama Canal, and the Bocas del Toro archipelago. We used metabarcoding with high throughput sequencing (HTS) with the V4 hypervariable region of the ribosomal gene complex (rDNA). We detected many protistan taxa, including a variety of parasitic and toxic taxa. There were 1,296 OTUs shared across all three regions, with an additional 342–1,526 OTUs occurring across two or more regions, suggesting some mixing within the Caribbean and across the Isthmus. In general, this mixing did not impact community similarity, which was primarily distinct across regions. When OTUs identified as gregarines were analyzed separately, most samples still grouped by region and there was no overlap of communities on either side of the Canal. Shipping traffic through the Panama Canal could move some taxa across regions; however, different environmental conditions in the two oceans may limit their establishment. Overall our results suggest that contemporary protistan biogeographic patterns are likely caused by a complex combination of factors, including anthropogenic dispersal and environmental tolerance.
