Single-cell transcriptomics reveals functional insights into a non-model aquatic phytoflagellate and its metabolically linked bacterial community

Single-cell transcriptomics is a vital tool for unraveling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with growth phases. Unexpectedly, a third transcriptional state was identified, across both growth phases. Metabolic mapping revealed a down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism from fast to slow growth to the third transcriptional state. Using carry-over rRNA reads, taxonomic identity of Ochromonas triangulata was re-confirmed and distinct bacterial communities associated with transcriptional states were identified. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability for uncovering ecological roles, surpassing alternative methods like metagenomics or metatranscriptomics.