We found that in the phosphate (PO4)‐depleted western subtropical North Atlantic Ocean, small‐sized pigmented eukaryotes (P‐Euk; < 5 μm) play a central role in the carbon (C) cycling. Although P‐Euk were only ~ 5% of the microbial phytoplankton cell abundance, they represented at least two thirds of the microbial phytoplankton C biomass and fixed more CO2 than picocyanobacteria, accounting for roughly half of the volumetric CO2 fixation by the microbial phytoplankton, or a third of the total primary production. Cell‐specific PO4 assimilation rates of P‐Euk and nonpigmented eukaryotes (NP‐Euk; < 5 μm) were generally higher than of picocyanobacteria. However, when normalized to biovolumes, picocyanobacteria assimilated roughly four times more PO4 than small eukaryotes, indicating different strategies to cope with PO4 limitation. Our results underline an imbalance in the CO2 : PO4 uptake rate ratios, which may be explained by phagotrophic predation providing mixotrophic protists with their largest source of PO4. 18S rDNA amplicon sequence analyses suggested that P‐Euk was dominated by members of green algae and dinoflagellates, the latter group commonly mixotrophic, whereas marine alveolates were the dominant NP‐Euk. Bacterivory by P‐Euk (0.9 ± 0.3 bacteria P‐Euk−1 h−1) was comparable to values previously measured in the central North Atlantic, indicating that small mixotrophic eukaryotes likely exhibit similar predatory pressure on bacteria. Interestingly, bacterivory rates were reduced when PO4 was added during experimental incubations, indicating that feeding rate by P‐Euk is regulated by PO4 availability. This may be in response to the higher cost associated with assimilating PO4 by phagocytosis compared to osmotrophy.

The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.