Diel Gene Expression of Eukaryotic Microplankton in the North Pacific Subtropical Gyre: Metatranscriptomic Windows into Temporal Function, Ecology, and Evolution of Uncultured Microbes

The oligotrophic waters of the North Pacific Subtropical Gyre host a diverse community of eukaryotic microplankton, including phototrophs, heterotrophs, and mixotrophs. To understand the daily rhythms of eukaryotic gene expression, we followed a Langrangian drifter near Station ALOHA and collected metatranscriptomes samples every 4 hours over a 4-day sampling period. Illumina deep sequencing and de novo assembly of poly-A+ selected metatranscriptomes yielded over 30 million contigs with an N50 of 423 base pairs. Taxonomic and functional annotations were assigned to 54% and 25% of contigs, respectively. Dimensionality reduction of known genetic features produces a statistical map of this transcriptional space, with organismal lineage and trophic level as major determinants. In this space, deviations from expected placements by some taxa suggest novel or divergent genetic capabilities. We also tested protein families for significant diel periodicity, revealing differences in the magnitude of diel regulation between taxa. Haptophytes, notably orders Prymnesiales and Phaeocystales, demonstrate the highest extent of diel transcript regulation. Dinoflagellates, with the exception of the basal parasitoid order Syndiniales, exhibit minimal diel regulation of their transcripts in contrast to other eukaryotes. Despite these differences, we have identified a core subset of protein families which are diel-regulated across diverse eukaryote lineages. The processes encoded by this core subset include light-harvesting, genetic regulation, electron transport, cell cycle, cytoskeletal elements, and transporters. Enrichment analysis of diel protein families in KEGG pathways reveals pathway-level expression differences between taxa, illustrating lineage-dependent routes of nutrients and energy flow through microbial networks across the day-night cycle. We will discuss these and additional findings of microeukaryote diel gene expression in the oligotrophic surface ocean.