Water Column Sampling:
Water column sampling was performed on four cruises during the spring and the summer of 2011 and 2012 at the Bermuda Atlantic Time-series Study station (31’40°N 64’10°W, BATS) and in the mesoscale eddies found in the surrounding area of the Sargasso Sea. For each cruise, 2 stations were sampled, usually in the center of a mesoscale eddy and at BATS. The edge of the eddy was sample two times, as well. To be able to get a better reproducibility of data, each experiment was replicated.

For each experiment, seawater samples were collected pre-dawn (on deck 2:30-4:00, local time) at four different depths within the euphotic zone (20m, 50m, 80m and the Deep Chlorophyll Maximum, DCM). Twenty-one 10L Niskin bottles were attached to a rosette with conductivity, temperature, depth sensors (CTD), and an in vivo fluorometer. This sensor allowed for recording in real time of chlorophyll fluorescence and the DCM for each station. The water that was collected from the 10L Niskin bottles was sampled for abundance and biomass of the plankton community.

Microscopy Analyses:
Inverted microscopy was used to determine abundance and biomass of planktonic ciliates. Seawater was collected into 200ml amber glass bottles which had previously been supplied with 2.5% of Lugol’s dye (v/v). Samples were stored in the dark and at room temperature onboard ship and in the laboratory at ASU. 100 ml of sample were settled onto settling chambers for 48hr according to the Utermöhl method (Utermöhl, 1931). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide and all the ciliates found were measured and classified based on the classification system introduced by Agatha (2004) and Agatha & Struder-Kypke (2007). Ciliates were classified into 4 standard shapes: prolate spheroid, sphere, cone, cone + half sphere.

Biomass calculations were done for each category of organism counted. Biovolume for each group was determined based on size and shape of the organism by approximating the closest geometric shape (Hillebrand et al. 1999) and then converted into units of carbon based on the carbon to volume ratio (Menden-Deuer and Lessard 2000). To determine the carbon biomass of the ciliates, carbon to volume conversion factors were used, as in Putt and Stoecker (1989). The 95% confidence intervals were calculated according to Lund et al. (1958).