Figure 1. Density (σ_θ; kg m^-3), oxygen (µmol kg^-1) and fluorescence (RFU) profiles at BATS station from March 2016 to December 2018. Thin, vertical lines indicate sampling events. Density and oxygen profiles are 0-1000 m, meanwhile fluorescence is shown only in the epipelagic (0-200 m). Mixed Layer Depth (MLD) is indicated by a white line in the density profile. The oxygen minimum zone is defined as the region with less than 160 µmol kg^-1, delineated with a black line in the oxygen profile.

Figure 2. Assignment for each sampled depth, at each month, to the community-composition based on non-hierarchical clusters for K =2 (upper panel) and K =9 (middle panel). K =2 separates the epipelagic and the mesopelagic, meanwhile K =9 reflects the epipelagic seasonality and depth-stratification. The lower panel shows the assignment of each sample to the 11 hydrographic layers defined by Curry et al. (see text). Blue bars correspond to deep mixing events, black bars to uplift of the deeper layers due to the passage of eddies.

Figure 3. PCoA ordination of all samples for the first two axis, based in their community composition. Environmental factors over imposed as vectors, with length corresponding to ρ. The circle represents ρ=1. Colors indicate the non-hierarchical cluster for each sample, forK =2 (upper panel) and K =9 (lower panel).

Figure 4. Taxonomic composition (at clade level) for each non-hierarchical cluster at K =2 (top) and K =9 (bottom). The parasitic order Syndiniales is highlighted within the Alveolata, showing its dominance within this phylum.

Figure 5. Functional profile (red: heterotroph, orange: mixotroph, green: autotroph) for each of the main components of the nine clusters, as indicated by the SIMPER analyses (after removal of parasitic lineages). When the V4 region was shared among lineages with different profiles, the corresponding colors are indicated in the bar.

Figure 6. PCoA ordinations for samples from surface (upper left), Chl-a maximum (upper right), 600 m depth (lower left) and 800 m depth (lower right), with ANOSIM R values for factor “seasons” indicated for each graph, and colors indicating seasons. In the epipelagic, a seasonal signal was detected, especially in the upper layers. In the mesopelagic (lower panels) no seasonality was observed, and samples diverging from the center core at these depths corresponded however to the uplifting events due to the passage of hydrographic features (within the squares).

Figure 7. Box and whiskers graphs for the distribution of the number of taxa (S), Shannon’s H, Faith PD and Pielou’s J for all samples from each cluster at K =9. Boxes indicate median, first and third quartiles.