<p>The intricate morphologies of the silica cell walls of diatoms are genetically controlled, as each species has its own unique ornamentation. The process of diatom silicification, from the initial uptake of soluble silicate from the environment, through the cellular deposition and morphogenesis of the mature silica element, is orchestrated by an array of macromolecules. It was recently shown that dAnk proteins, which are involved in silica formation, are regulators of the silica pore pattern. In this work, we study the influence of another controller, silicate availability in the environment, on silica phenotype in dAnk knockout mutants. Using various microscopy techniques, we show that the phenotype of some mutants is variable, ranging from large gaps in the silica to pore-less silica coverage. In situ cryo-electron tomography shows that not only is morphogenesis affected, but also the regulation of the silica deposition vesicle is altered. These results point to an additional role of the dAnk proteins, where they are involved in the regulation of intracellular silicification, and when their expression is disrupted, silicification becomes sensitive to silicate availability. This points to synergistic regulation of silicification, where the function of a specific protein is context-dependent.</p>