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Background  Microalgae are potential sources of biofuels and high-value compounds. Mixotrophic conditions usually promote growth of microalgae. The pennate diatom  Phaeodactylum tricornutum , with its short life cycle, completely sequenced genome, and ease of transformation, can be used as a model for studying carbon metabolism in microalgae.    Results  We compared the growth rate of  P. tricornutum  (IOCAS-001) under different conditions and labeled the cells using [ 13 C]glycerol (GL). The results revealed GL promoted the growth of  P. tricornutum . Ser and Gly were synthesized via photorespiration. The  13 C enrichment of Ser and Gly under nitrogen-limited conditions was much higher compared to other amino acids, indicating the enhancement of photorespiration. Addition of sodium acetate decreased the growth rate of  P. tricornutum  under nitrogen-limited conditions. Our results indicated that the GL carbon backbone enters the Calvin cycle in the form of dihydroxyacetone phosphate (DHAP), producing xylulose 5-phosphate (X5P) with a GL2_3-generated carbon backbone distributed at X5P1_2 and ribose 5-phosphate (R5P) with GL1-derived carbon atoms at R5P1 and R5P2. Both R5P and X5P can be converted into ribulose-1,5-bisphosphate (RuBP). By oxygenation of RuBP carboxylase/oxygenase (Rubisco) and metabolism through photorespiration, these RuBPs generate Ser and Gly with GL1 or GL2-derived carbon atoms at position 1 and GL1 or GL3-derived carbon atoms at other positions, resulting in a low level of  13 C enrichment of Gly1 and Ser1.    Conclusion  Our results indicated different strains of  P. tricornutum  have different mechanisms for organic carbon metabolism. Photorespiration is involved in GL metabolism and is important for the nitrogen-limited response in  P. tricornutum .    Classification  Metabolic flux analysis, microalgae    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0256-5) contains supplementary material, which is available to authorized users.

Phaeodactylum tricornutum photorespiration takes part in glycerol metabolism and is important for nitrogen-limited response