In this work, a cooperative algal-bacterial system that efficiently degrades thiocyanate (SCN-), a toxic contaminant, and exhibits high lipid productivity, was developed. A consortium of mixed bacteria (activated sludge) and microalgae was sequentially cultivated under photoautotrophic and photoheterotrophic modes. The hydrolysis of SCN- to ammonium (NH4+)-nitrogen and subsequent nitrification steps were performed by the initial activated sludge under lithoautotrophic conditions. The NH4+ and oxidized forms of nitrogen, nitrite (NO2-) and nitrate (NO3-), were then assimilated and removed by the microalgal cells when light was supplied. After the degradation of SCN-, the cultivation mode was changed to photoheterotrophic conditions in a sequential manner. Algal-bacterial cultures containing Chlorella protothecoides and Ettlia sp. yielded significantly increased lipid productivity under photoheterotrophic conditions compared to photoautotrophic conditions (28.7- and 17.3-fold higher, respectively). Statistical methodologies were also used to investigate the effects of volatile fatty acids and yeast extract on biomass and lipid production. (C) 2014 Elsevier Ltd. All rights reserved.