Metabolic Modeling of a Model Diatom

Diatoms are unicellular photosynthetic microalgae that are ubiquitous in fresh water and marine and environments. These microalgae are amenable for ~20% of the global carbon fixation. Diatoms are highly diverse and have substantially higher productivity and capabilities to accumulate lipids compared to other classes of microalgae. These properties make diatoms ideal candidates for advanced production of biofuels and chemicals. However, metabolism of diatoms is poorly characterized both in laboratory settings as well as in the environment, where diatoms interact. Previous studies revealed a very high abundance of marine viruses, some of which have been shown to infect diatoms along with other phytoplankton cells, and thus altering their metabolism. To gain in-depth knowledge about diatom metabolism and to address how viral infection modifies diatom physiology, we applied constraint-based modeling to the model diatom Cylindrotheca at different physiological states during its life-cycle. A genome-scale metabolic model of Cylindrotheca has been generated using annotated genome and three previously developed metabolic reconstructions of photosynthetic organisms (Phaeodactylum tricornutum, Chlamydomonas reinhardtii, and Chlorella vulgaris) as template database of biochemical reactions. The model is validated with growth/no growth physiological data at several growth conditions. Furthermore, the model is constrained using single-cell RNA-sequencing data with and without viral infection to elucidate the involved mechanisms in viral infection to Cylindrotheca. Metabolic model integrated with time-course gene expression data is employed to explore the physiological characteristics, such as growth and lipid biosynthesis at different stages, and to determine how viruses affect the metabolism of the diatom host at these states. The outcome of this work will underpin future studies to advance our understanding of diatom metabolism and to elucidate their role on the ecology and biogeochemistry of the ocean.