The genus Nannochloropsis comprises a group of oleaginous microalgae that accumulate polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA). These molecules are essential for the correct development and health of humans and animals. Thanks to their attractive lipid profile, Nannochloropsis is mainly marketed as a feed ingredient in aquaculture. In microalgae of this genus, contents and cellular location of PUFAs are affected by the growth conditions and gene expression. Strain improvement through non-recombinant approaches can generate more productive strains and efficient bioprocesses for PUFA production. Nevertheless, the lack of specific markers, detection methods, and selective pressure for isolating such mutants remains a bottleneck in classical mutagenesis approaches or lipid quality assessment during cultivation. This review encompasses the importance of PUFAs and lipid classes from Nannochloropsis species and their potential applications. Additionally, a revision of the different ways to increase PUFA content in Nannochloropsis sp. by using classical mutagenesis and adaptive laboratory evolution is also presented, as well as various methods to label and quantify lipids and PUFAs from Nannochloropsis microalgae.

Commercial production of eicosapentaenoic acid (EPA) from photoautotrophic microalgae like Nannochloropsis oceanica requires higher productivity and larger scales to reduce costs. Improving productivity can be achieved by increasing biomass concentrations, which creates light gradients in the reactor depending on the culture’s acclimation and the reactor geometry. These light gradients affect physiology, lipid synthesis, but also the distribution of fatty acids between lipid classes. In this study we evaluated the combined effect of the incident light intensity and light gradient on growth, biochemical composition, and fatty acid distribution between lipid classes. A total of 13 cultivations were performed in continuous mode using three different incident light intensities (200, 670, and 1550 μmol photons m⁻² s⁻¹) and four dilution rates (from 0.29 to 0.75 day⁻¹). Reducing dilution rates resulted in higher biomass concentrations, steeper light gradients, and lower average light intensities. Increasing incident light intensity improved biomass productivity from 0.5 to 1.8 g L⁻¹ day⁻¹, while the biomass yield on light decreased from 1.05 to 0.44 g mol⁻¹. Lowering average light intensities decreased the triglyceride content from 11.1 to 1.5% w/w, and increased the galactolipid content, mainly monogalactosyldiacylglycerol, up from 3.1 to 5.1% w/w. Total EPA contents did not decrease at low incident light but decreased by 28% at highly saturating light, both relative to medium incident light. The EPA content in polar lipids increased at lower average light intensities, and decreased in the neutral fraction simultaneously. These results highlight the tight regulation of EPA content between lipid polar and neutral fractions under different light regimes. Graphical Abstract

Summary: Oleaginous microalgae, such as Nannochloropsis oceanica , hold strong promise for sustainable lipid bioproduction, but fully realizing this potential requires systems-level insight into their complex metabolism. One of the central challenges in optimizing lipid productivity is the resolution of the highly heterogeneous and incompletely annotated metabolic networks, which respond dynamically to strain-specific traits and cultivation conditions. Here we present iSO1949_N.oceanica, the first genome-scale constraint-based metabolic model (GEM) for this species. Constructed through an orthology-based approach using curated models of related microalgae, the GEM integrates core photosynthetic metabolism and lipid biosynthesis pathways with extensive subcellular localization predictions. To capture environmental dynamics, we introduce two light-acclimation modes derived from continuous cyclostat cultivations, incorporating biomass composition, oxygen exchange, and maintenance rates based on photosynthesis–irradiance curves. Simulations reproduce carbon assimilation under variable light conditions and differentiate acclimated phenotypes. iSO1949_N.oceanica provides a comprehensive framework for exploring photosynthetic metabolism and guiding engineering strategies under photobioreactor-relevant conditions. This resource advances the use of N. oceanica as a chassis for sustainable lipid production and establishes a foundation for systems-level analysis of stramenopile microalgae.