## 2 Materials and Methods
### Germinatin of H. pluvialis Cyst Cells  
For germination, aliquots of the cyst cells were cultivated as described in Section 2.2 and centrifuged at 5500 rpm. The supernatant was removed and the biomass was washed with distilled water, centrifuged again, and the supernatant discarded. The cyst cells were germinated under a phototrophic, mixotrophic, or heterotrophic culture. The cyst cells were suspended in 200 mL BBM and 4 mM glucose was added to the mixotrophic or heterotrophic cultures. In a preliminary study, ribose, sodium acetate, and glucose were tested for mixotrophic cyst cell germination. More zoospores were released using glucose compared to ribose and sodium acetate (Figure S1) and enhanced germination of cyst cells were observed at these carbon concentrations compared to phototrophic germination. Additionally, in a preliminary study, glucose concentrations of 4, 8, 20, and 40 mM were used for mixo- and heterotrophic cyst cell germination, and the glucose concentration did not affect the germination efficiency (Figure S2). Thus, concerning resource consumption, the lowest investigated glucose concentration of 4 mM was used in the further course of experiments. Where germination was carried out with artificial light, \"red light\" was used, with light intensity as shown in Table 1.  
Figure 2: Photobioreactor HDC 1.100B filled with _H. pluvialis_ cells at different cell stages.  
Four sets of experiments were carried out. In each set, four germination experiments were performed at different conditions using the same batch's cyst cell biomass. Thus, the \"internal\" state (nitrate, lipid, starch, astaxanthin content, etc.) of the cyst cells differs at the beginning of the germination for each set of experiments. Therefore, it is more reasonable to evaluate the tendencies within one set of an experiment than to compare absolute values between different sets of experiments. In the first set of experiments, the influence of gassing with 3% \(v/v\) CO\({}_{2}\) compared to cultivation at ambient air was examined using phototrophic culture 1 and 2 and mixotrophic culture 3 and 4 at 100 \(\upmu\)mol m\({}^{-2}\) s\({}^{-1}\). Germination conditions of cultures 1 to 4 were repeated using a light intensity of 75 \(\upmu\)mol m\({}^{-2}\) s\({}^{-1}\) and are presented in Table 1 as culture 5 to culture 8. In the third set of experiments, cultures 9 to 12, the conditions of cultures 6 and 8 at 75 \(\upmu\)mol m\({}^{-2}\) s\({}^{-1}\) were repeated (cultures 11 and 12). In addition, these two experiments were carried out in darkness by covering the reactors with aluminum foil for heterotrophic germination. Glucose was added to culture 10, while no further external carbon source was added to culture 9.  
In the fourth and last series of experiments (cultures 13 to 16), all the cultures were germinated in the presence of 4 mM glucose. In cultures 14 and 16 additional sodium nitrate was added, resulting in a nitrate concentration two times higher than the one in the BBM medium. Cultures 13 and 14 were germinated in darkness. Cultures 15 and 16 were first germinated in the presence of red light, at a light intensity of 75 \(\upmu\)mol m\({}^{-2}\) s\({}^{-1}\). After the nitrate consumption (25 h after the start of the germination) the germination was continued in complete darkness.