.representing > 45% of TOC at all sampled timepoints (Table.1). This has also been observed in other carbon budgets of Phaeodactylum [34] and [52]. The protein content of the cells only changed by ~ 20% throughout the day and reached a maximum value of 11.07 ± 0.85 pg cell− 1 in the middle of the afternoon (Fig. 3E, n = 4). Total proteins per cell dropped from 10.00 ± 0.63 pg cell− 1 at dusk to 8.10 ± 0.29 pg cell− 1 at 2nd dawn (Fig. 3). However, assuming an even redistribution between daughter cells after division, some proteins had to be synthesized during the night to reach such values at 2nd dawn. The drop in cellular carbon associated with carbohydrate and TAG may be enough to explain the redistribution of carbon skeletons from these cellular pools to protein. We did not measure polar lipids in this study but it is possible that they represent a large portion of the carbon budget [47]. Galactolipids, which are integral components of the thylakoid membranes, are consumed in the dark in other algae [55] and [56]. Our results suggest that dark catabolism in diatoms may represent a complicated interplay between lipid, carbohydrate and protein breakdown and biosynthesis.