V4 ribosomal gene amplicon sequencing to determine protistan community diversity at two sites in Waquoit Bay, Massachusetts. The study was carried out in the summer of 2019 at the river influenced site (Childs River) at the top of the bay, and the coast ocean site at bottom of the bay, to examine the impact of nitrogen on community profiles. Incubation experiments with bromodeoxyuridine labeled bacteria were also carried out, and the immunoprecipitated DNA amplified and sequenced to identify putative mixorophic algae.