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Phytoplankton on the Scotian Shelf (SS) are well studied using microscopy and flow cytometry (FCM). These tools provide a picture of a diatom dominated spring bloom, and summer–autumn communities dominated by the cyanobacterium Synechococcus. FCM studies have shown that non-diatom microbial eukaryotes are present throughout the year, but the diversity and seasonality of these often smaller difficult to identify species are not well known. We investigated the taxonomic identity of surface and sub-chlorophyll maxima communities, using cloning and sequencing of the 18S rRNA gene, in April and October, along two inshore to offshore transects. Here, we report new taxonomic records and evidence of novel taxa in this well-studied system. For example, during April, previously unreported Phaeocystis spp. were recovered and picophytoplankton ‘patches’ identified from FCM were marked by the Bolido-Parmales complex. The October communities were phylogenetically diverse with chlorophytes more prevalent. Among heterotrophic taxa, choanoflagellates were characteristic of April along with two clades of uncultivated marine stramenopiles (MAST) clades; MAST-7 and MAST-1. In contrast, MAST-4 was more prevalent in October. There were also onshore versus offshore differences, with the April offshore communities more similar to October communities, reflecting nutrient draw-down and a post-bloom community offshore in April.

Phylogenetic diversity of eukaryotic marine microbial plankton on the Scotian Shelf Northwestern Atlantic Ocean