Microalgae are valuable resources for producing high-value compounds, but large-scale cultivation in open raceway ponds (ORPs) faces challenges due to salinity and temperature fluctuations, which affect biomass yield and quality. Developing strains with high productivity and stable quality across varying salinity and temperature levels offers a promising approach to overcoming these challenges. Cyclotella cryptica, a marine diatom species, is known for its robustness under diverse salinity conditions, but its biochemical composition and frustule morphology in respond to salinity remains largely unknown. Moreover, the responses of C. cryptica to temperature fluctuations are largely unexplored, posing a barrier to its industrial application in ORPs. In this study, C. cryptica was cultivated under six salinity levels (19–34 ‰ at 3 ‰ intervals) and five temperature regimes (17–33 °C at 4 °C intervals) to investigate the effects of these environmental factors on growth performance, macronutrient composition, fatty acid (FA) profile, and carotenoid content. Additionally, we examined the biosilica content, frustule morphology, and the transcriptional levels of five frustule biogenesis related genes (CcSin1, CcSin2, and CcSAP1–3) to assess the impact of salinity and temperature on the biosilification process. Our findings revealed that salinity exerts minimal effects on growth, macronutrient composition, FA profile, and carotenoid content, whereas it induces significant variations in frustule morphology and biosilica deposition. In contrast, temperature markedly influences all evaluated parameters. These insights into the adaptive mechanisms of C. cryptica to salinity and temperature variations are crucial for optimizing the scale-up cultivation strategy of this species in ORPs.
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