| Summary: | Phytoplankton synthesizes essential ω-3 and ω-6 polyunsaturated fatty acids (PUFA) for consumers in the aquatic food webs. Only certain phytoplankton taxa can synthesize eicosapentaenoic (EPA; 20:5ω3) and docosahexaenoic acid (DHA; 22:6ω3), whereas all phytoplankton taxa can synthesize shorter-chain ω-3 and ω-6 PUFA. Here, we experimentally studied how the proportion, concentration (per DW and cell-specific), and production (µg FA L<sup>-1</sup> day<sup>-1</sup>) of ω-3 and ω-6 PUFA varied among six different phytoplankton main groups (16 freshwater strains) and between exponential and stationary growth phase. EPA and DHA concentrations, as dry weight, were similar among cryptophytes and diatoms. However, <i>Cryptomonas</i><i> </i><i>erosa</i> had two–27 times higher EPA and DHA content per cell than the other tested cryptophytes, diatoms, or golden algae. The growth was fastest with diatoms, green algae, and cyanobacteria, resulting in high production of medium chain ω-3 and ω-6 PUFA. Even though the dinoflagellate <i>Peridinium</i><i> </i><i>cinctum</i> grew slowly, the content of EPA and DHA per cell was high, resulting in a three- and 40-times higher production rate of EPA and DHA than in cryptophytes or diatoms. However, the production of EPA and DHA was 40 and three times higher in cryptophytes and diatoms than in golden algae (chrysophytes and synyrophytes), respectively. Our results show that phytoplankton taxon explains 56%–84% and growth phase explains ~1% of variation in the cell-specific concentration and production of ω-3 and ω-6 PUFA, supporting understanding that certain phytoplankton taxa play major roles in the synthesis of essential fatty acids. Based on the average proportion of PUFA of dry weight during growth, we extrapolated the seasonal availability of PUFA during phytoplankton succession in a clear water lake. This extrapolation demonstrated notable seasonal and interannual variation, the availability of EPA and DHA being prominent in early and late summer, when dinoflagellates or diatoms increased.
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