Microalgae are considered excellent organisms for biofuel source for abundant neutral lipids. However, the traditional gravimetric method has the problems of long measuring time and dangerous reagent. Therefore, a rapid and safer quantification method Nile red method was applied in Chlorella sp. L166. This study exams the influenced factors for Nile red method: emission wavelength, excitation wavelength, voltage, slit, Nile red concentration and staining time were 534 nm, 576 nm, 700 V, 5.0 nm, 4.0 μg/mL and 10 min, respectively. The fluorescence intensity of different concentration algal solution (OD680 = 0.2–1.2) showed a good correlation. Compared with the gravimetric method, there was no significant difference between these two methods. Fluorescence intensity stained with Nile red got reproducible results. The method could determine the lipid concentration in a short-time (measurement time was reduced by 13 times) and its safer, it might be a promising alternative for rapid lipid measurement in Chlorella sp.
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