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PC is a bioactive and colorant compound widely sought in the food, nutraceutical and cosmetic industries, and one of the most important pigments produced by Synechocystis salina. However, the general extraction process is usually time-consuming and expensive, with low extraction yields—thus compromising a feasible and sustainable bioprocess. Hence, new extraction technologies (e.g., ultrasound assisted-extraction or UAE) emerged in the latest years may serve as a key step to make the overall bioprocess more competitive. Therefore, this study aimed at optimizing the yields of phycocyanin (PC) rich-extracts of S. salina by resorting to UAE; in attempts to explore this process in a more economically feasible way; valorization of the remaining cyanobacterial biomass, via extraction of other bioactive pigments and antioxidants, was tackled within a biorefinery perspective. A two-stage extraction (using ethanol and water) was thus performed (because it favors PC extraction); other bioactive pigments, including chlorophyll a (chl a), carotenoids, and other phycobiliproteins (PBPs), but also antioxidant (AOX) capacity and extraction yields were also evaluated for their optimum UAE yields. A factorial design based on Box–Behnken model was developed; and the influence of such extraction parameters as biomass to solvent ratio (B/S ratio = 1.5–8.5 mg·mL−1), duty cycle (DT = 40–100%), and percentage of amplitude (A = 40–100%) were evaluated. The model predicted higher PC yields with high B/S ratio = 6 mg·mL−1, lower DT = 80% and an A = 100%. Classical extraction was compared with UAE under the optimum conditions found; the latter improved PC yields by 12.5% and 47.8%, when compared to freeze-thawing extraction, and bead beater homogenization-based extraction, respectively. UAE successive extractions allowed to valorize other important bioactive compounds than PC, by reusing biomass, supporting a favorable contribution to the economic feasibility of the S. salina-based process towards a biorefinery approach.

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