Abundance of eukaryotic microbes in the deep subtropical North Atlantic

The meso- and bathypelagic ocean comprises the largest habitat on earth, yet we know very little about the distribution and activity of protists in this environment. These small eukaryotes are responsible for controlling bacterial abundance in the surface ocean and are major players in the material and energy transfer of pelagic food webs. In this paper, we quantify microbial eukaryotes in the deep North Atlantic, as well as provide a basic characterization of eukaryote community changes through the water column. To this end, we counted organisms using 2 different approaches: (1) catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH, also known as TSA-FISH) with the EUK516 probe and the newly developed KIN516 probe for kinetoplastids, and (2) 4',6-diamidino-2-phenylindole in combination with fluorescein isothiocyanate staining (DAPI-FITC). We performed several tests to compare the abundances measured by these 2 methods, and quantified losses at each step in the process. We also used the morphology of nuclei stained with DAPI as a quick method to characterize some groups of protists. We found that eukaryotes and kinetoplastids both decreased in abundance with increasing depth at a greater rate than bacteria or viruses. Below 1000 m and to the maximum depth collected in this study (i.e. 5000 m) the concentration of eukaryotic microbes counted using both methods remained constant. Kinetoplastids represented a significant fraction (average 21.8%) of total eukaryotic microbes counted by CARD-FISH throughout the water column, and this percentage increased somewhat with depth. One unique yet unidentified nuclear morphotype as identified by DAPI staining remained equally abundant throughout the entire water column, and was the most abundant protist in deep-sea samples