Unicellular eukaryotes are responsible for a massive amount of photosynthetic carbon fixation in marine systems. The smallest among these fall within the “pico” size fraction (<2 micrometers in diameter), are broadly distributed – from coastal to open-ocean environments – and are highly diverse. Picoeukaryotes contribute a significant proportion of the biomass and primary production within this size fraction, often rivaling their cyanobacterial counterparts Prochlorococcus and Synechococcus. Despite the importance of these eukaryotic phytoplankton, research on their distributions and genetic capabilities has consistently lagged behind that on their bacterial counterparts. This lag persists even now due to their larger genome sizes, tremendous diversity and difficulties in isolating and culturing many of the taxa. Micromonas pusilla is one of the most widespread picoeukaryotic species. This photosynthetic alga thrives from tropical to polar marine ecosystems and belongs to an anciently diverged clade (prasinophytes) sister to land plants. We sequenced complete genomes of two strains within this purported ‘species,’ and found far greater genome variability than anticipated based on their high 18S rRNA gene identities. The Micromonas strains have striking differences in terms of gene content, invasion elements and aspects of gene regulation. Genes in each that are mutually exclusive, i.e. ‘niche defining genes’, have phylogenetic profiles that are dissimilar from ‘core’ genes, pointing to different selection and acquisition processes. Data from field expeditions show that in addition to prasinophytes, several uncultured lineages are also important components of the photosynthetic picoeukaryotic community. Collectively, these data highlight challenges for metagenomic analyses and reshape how we approach picoeukaryotic populations in situ. Our findings underscore the potential for refined metagenomic approaches to facilitate development of testable hypotheses on population controls of these important primary producers.
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