The microalgae of watermelon snow: culture and de novo genome of Sanguina aurantia

During the melt season, blooms of microalgae appear on alpine and polar snowfields. Chlorophytes that synthesize astaxanthin cause red snow, known globally as the phenomenon 'watermelon snow'. Snow algae darken the snow surface and decrease albedo, this in effect increases melt and can accelerate the decline of snow environments already at-risk due to global warming. The snow algae environment is an ephemeral habitat characterized by low temperatures around 0 °C and high light intensity at the snow surface up to 5000 µmol m−2 s−1 PAR (photosynthetically active radiation). These conditions make photosynthesis and maintaining photo-stasis a challenge for the algae. Little is known on how snow algae colonize and thrive on the snow surface due to difficulties cultivating the cells and the lack of high-quality genomic data. For this reason, the first aim of my thesis was to cultivate a snow alga from red blooms. After dozens of cultivation attempts, we grew green biciliates conspecific with the spherical orange, immotile cells of Sanguina aurantia. The cosmopolitan genus Sanguina is often dominant in red blooms and the availability of a culture provided me with opportunity for my second thesis aim: to assemble a high-quality snow algal genome. Utilizing Oxford Nanopore Technology, Illumina sequencing, and high-throughput chromatin conformation capture (Hi-C) with the green biciliate culture as source material, I assembled a de novo genome of S. aurantia. Supported with RNA-sequencing, I provide insight into the annotation and architecture of a snow algal genome and outline the value of hybrid assemblies when working with a culture grown from a field sample. Blooms are diverse and an array of 'red-jeweled' cells are often present. Historically, all red cells were phylogenetically grouped, and some thick-walled rosette-like cells were thought to be life stages of other species. The third aim of my thesis was to assess the taxonomic position of distinct rosette morphologies. Single-cell sequencing revealed five morphotypes that form their own novel genus, which we designate Rosetta. By presenting a novel genus and a de novo snow algal genome, this thesis advances techniques in species identification and sets the foundation for future genomic studies.