BACKGROUND: This paper reports the results of an experimental campaign of autotrophic cultures of Stichococcus strains aiming at selecting the most promising strain for biofuel production. The strain selected - S. bacillaris 158/11 - was cultivated in 1 L lab-scale bubble column photobioreactors under fed-batch and semi-continuous conditions. A Bold basal medium supplemented with NaNO(3) as nitrogen source was adopted. Tests were carried out at 23 degrees C, 140 mu E m(-2) s(-1), and air flow rate ranging between 0.4 and 4 vvm. Cultures were characterized in terms of pH, concentration of total nitrogen, total organic carbon, total inorganic carbon, biomass, lipid fraction and methyl-ester distribution of transesterified lipids. RESULTS: S. bacillaris 158/11 proved to be the best strain to produce biodiesel. Methyl-ester distribution was characterized by a large fraction of methyl palmitate, methyl linolenate, methyl linoleate, and methyl oleate along with phytol. The process photosynthetic efficiency - fraction of available light stored as chemical energy - was about 1.5%. Specific biomass productivity was similar to 60 mg(DM) L(-1) day(-1) under the semi-continuous conditions tested. Total lipid productivity was 14 mg L(-1) day(-1) at a dilution rate of 0.050 L day(-1). CONCLUSION: S. bacillaris 158/11 is a potential strain for massive microalgae cultures for biofuel production. Higher biomass/total-lipid productivity could be obtained in sunlight. (C) 2011 Society of Chemical Industry