This study investigated the treatment of unsterilized, undiluted, and unfiltered liquid digestate in a large-scale photobioreactor over a period of 33 weeks using a consortium of microalgae and bacteria. The generated biomass was analyzed for a wide spectrum of value-added compounds. The impact of organic loading rates (OLR) on the microbial culture was determined, and the influence of the biomass storage method on its qualitative composition was also analyzed. The experiment showed optimal growth of microalgae at OLR = 0.1 gCOD/L/day (where COD is Chemical Oxygen Demand), while a higher OLR value led to culture destabilization. Microglena sp., an algae not commonly applied for digestate treatment, showed low tolerance to changes in process conditions (OLR increase) but high readaptation potential when the OLR was lowered to its initial value. Significant changes in the microbial community were observed during the treatment. In Phases 1 and 2, Desmodesmus subspicatus and Actinomycetota phylum dominated in the community, while in Phase 3, Microglena sp. and Firmicutes were the most abundant. Total nitrogen, orthophosphates, and soluble COD were reduced by 89–99%. The biomass storage method had a notable impact on the content of lipids, fatty acids, and pigments. The protein amount was 32.75–33.59% of total solids (TS), while total lipid content was 15.76–19.00% TS, with stearic and palmitic acid being dominant. The effect of the storage regime on the potential biomass valorization was also discussed.

Temperature and light intensity are among the most influential environmental factors modulating cyanobacterial physiology, yet their interactive effects on metabolite accumulation remain understudied in several genera with biotechnological potential. In this study, the influence of temperature (12, 20 and 28 °C) and light intensity (60, 120 and 180 µmol photons m ⁻² s ⁻¹ ) on the growth, pigment profile, and lipid composition of two Aphanothece strains ( A. microscopica and A. stagnina ) was evaluated through a 3 ² full factorial design. Both species exhibited strain-specific responses across all measured parameters. In A. microscopica , high temperature and low light promoted the accumulation of chlorophyll a , phycobiliproteins (particularly phycocyanin and allophycocyanin), and a diversified carotenoid profile including echinenone and myxoxanthophyll. In contrast, A. stagnina showed higher pigment productivity under high temperature combined with high irradiance, particularly enriching zeaxanthin and β-carotene. Lipid content increased in both strains under low temperature and moderate light, suggesting a compensatory metabolic route under suboptimal growth conditions. Fatty acid analysis revealed major differences: A. microscopica displayed a complex profile dominated by palmitic acid and enriched with polyunsaturated fatty acids under cold treatments, while A. stagnina exhibited reduced diversity, with monounsaturated fatty acids, especially palmitoleic and myristic acids, prevailing under all conditions. These findings underscore the metabolic flexibility of Aphanothece species in response to environmental variation and highlight their differentiated potential for applications in biorefineries. Selective cultivation of each strain under tailored conditions may enhance the yield of specific pigments or lipids, supporting their use in biofuel, nutraceutical, and cosmeceutical industries. Graphical Abstract