This work evaluated biological effect of nC(60) on Scenedesmus obliquus. The cells were exposed to various concentrations of nC(60) for 7 days. Low-dose of nC(60) was found to have a minor growth inhibitory effect. The transcriptomics and metabolomics were integrated to examine intricate molecular and cellular effects of nC(60) on Scenedesmus obliquus. We found that Scenedesmus obliquus cells exposed to nC(60) had several significant alterations in cellular transcription and biochemical processes. During the 7-day exposure to nC(60), 2234 and 2,448 unigenes were differentially expressed by 0.1 mg/L and 1 mg/L nC(60)-treated groups compared with the control, including 2085 or 2247 up-regulated genes and 149 or 201 down-regulated genes, respectively. We successfully identified 22 metabolites, including 6 significantly changed metabolites, such as sucrose, D-glucose, and malic acid. The citrate cycle (TCA cycle) (ko00020) was the main target of both differentially expressed genes and metabolic change. However, accumulation of sucrose (end-product) could have induced feedback inhibition of photosynthesis in Scenedesmus obliquus, explaining the slight growth inhibition observed. The results provided a mechanistic understanding of the growth inhibition of nC(60) toxicity. These genes and metabolites are useful biomarkers for future studies and offer new insights into the early detectable changes in Scenedesmus obliquus with nC(60) exposure. (C) 2016 Elsevier B.V. All rights reserved.