Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad

Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised the first cultured representative of the freshwater Cryptomonad Group 1 (CRY1a) lineage using the genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwater. It is a small heterotrophic nanoflagellate (ca. 5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of loss of an ancestral photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to the acquisition of the red-algal symbiont in photosynthetic cryptophytes. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.