We programmed incident light to change as a sinusoidal wave over the course of the day. Light also varied from the surface of the illuminated culture to the bottom (Fig. 1).
The cells experienced a complex light environment due to the day/night cycle and also due to rapid vertical mixing from the constant stirring and sparging [25]. Our experiments started with approximately 2 × 106 Phaeodactylum cells mL− 1, a denser population than in natural habitats even during diatom blooms [43]. This led to self-shading effects and attenuation of light intensity through the 23 cm depth of the culture (Fig. 1, Fig. S1). Light attenuation with depth is also observed in large-scale photobioreactors or open ponds [44]. Additionally, the accumulation of biomass and cell pigments throughout the day increased the attenuation of light in the photobioreactor leading to a slightly asymmetrical pattern of light at the base of the culture (Fig. 1). Therefore our conditions mimicked light environments like those experienced by cells in a low density, well-mixed large-scale photobioreactor where cells are mixed turbulently through a broad gradient of light. Our conditions did not mimic conditions found in very dense cultures where cells will move rapidly between light and dark environments.