Cyanobacteria have been identified as promising organisms to reuse nutrients from waste effluents and produce valuable compounds such as lipids, polyhydroxyalkanoates (PHAs), and pigments. However, almost all studies on cyanobacterial biorefineries have been performed under lab scale and short cultivation periods. The present study evaluates the cultivation of the cyanobacterium Synechocystis sp. in a pilot scale 30 L semi-continuous photobioreactor fed with secondary effluent for a period of 120 days to produce phycobiliproteins, polyhydroxybutyrate (PHB) and lipids. To this end, the harvested biomass from the semi-continuous photobioreactor was transferred into 5 L vertical column batch photobioreactors to perform PHB and lipid accumulation under nutrient starvation. Three hydraulic retention times (HRT) (6, 8 and 10 days) were tested in the semi-continuous photobioreactor to evaluate its influence on biomass growth and microbial community. A maximum biomass concentration of 1.413 g L^-1 and maximum productivity of 173 mg L^-1 d^-1 was reached under HRT of 8 days. Microscopy analysis revealed a shift from Synechocystis sp. to Leptolyngbya sp. and green algae when HRT of 6 days was used. Continuous, stable production of phycobiliproteins in the semi-continuous photobioreactor was obtained, reaching a maximum content of 7.4%_dcw in the biomass. In the batch photobioreactors a PHB content of 4.8%_dcw was reached under 7 days of nitrogen and phosphorus starvation, while a lipids content of 44.7%_dcw was achieved under 30 days of nitrogen starvation. PHB and lipids production was strongly dependent on the amount of nutrients withdrawn from the grow phase. In the case of lipids, their production was stimulated when there was only phosphorus depletion. While Nitrogen and phosphorus limitation was needed to enhance the PHB production. In conclusion, this study demonstrates the feasibility of cultivating cyanobacteria in treated wastewater to produce bio-based valuable compounds within a circular bioeconomy approach.

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