Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean

Summary Close associations between single‐celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence‐activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N2)‐fixing cyanobacterium, UCYN‐A and its prymnesiophyte host was prevalent in both population and single‐cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species‐specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN‐A symbiosis, similar tight species‐specific associations with PPEs are unusual in the oligotrophic ocean.