Rapid method to screen and sort lipid accumulating microalgae

•Optimized method for detecting lipid rich cells of C. littorale with FACS.•Efficient BODIPY staining dissolved only in ethanol, no assistant necessary.•Maintenance of cellular viability after staining and cell sorting.•The process can be applied to sort cells with high lipid content.

The present work established an efficient staining method for fluorescence activated cell sorting (FACS) with Chlorococcum littorale maintaining cellular viability. The method was designed to detect high-lipid cells and to guarantee cellular viability. BODIPY505/515 (BP) was more suitable to FACS when compared to Nile red. The optimum concentrations were 0.4 μg ml−1 of BP, 0.1% DMSO or 0.35% ethanol. Both ethanol and DMSO were equally efficient and assured cellular viability after the staining and sorting. Here a method is presented to rapidly screen and sort lipid rich cells of C. littorale with FACS, which can be used to produce new inoculum with increased cellular lipid content.