The cultures of the snow alga Chlamydomonas nivalis in the exponential phage were stressed by NaCl (up to 1.5%) for 0 similar to 48 h, followed by Nile Red staining-based cytomic analysis (flow cytometry and confocal laser scanning microscopy). The fluorescent intensities of total lipids, and neutral and polar lipids increased to the maximum within 7 h in the NaCl stressed cells with the highest increase in total lipids by 2-fold (0.75%-NaCl for 7 h), the highest increase in neutral lipids by 68-fold (1%-NaCl for 7h) and the highest increase in polar lipids by 10-fold (1.25%-NaCl for 5 h), respectively. Seven types and 22 kinds of polar lipid molecules were selected and identified as biomarkers by UPLC/Q-TOF-MS-based lipidomic analysis, which demonstrated differences in total lipids between the stress group (0.75%-NaCl for 7 h) and the control. The biological roles of the biomarkers in the alga under NaCl stress were discussed. The integrated approach based on "omics" technologies developed in the present work is validated as a powerful tool to successfully reveal the regulation of lipid metabolism in microalgae in response to stress stimulation. (c) 2012 Elsevier Ltd. All rights reserved,