Engineering photosynthetic microorganisms in biofoundries: challenges and opportunities

Photosynthetic microorganisms can convert sunlight and CO₂ directly into biomass and bioproducts. Yet, most biofoundries still optimize heterotrophic chassis reliant on agricultural sugars, limiting impact on global decarbonization. This review argues that sustainable manufacturing requires integrating microalgae and cyanobacteria into Design-Build-Test-Learn pipelines and shifting from biomass conversion to light- and CO₂-driven production. We highlight advances in genetic and cellular engineering in model photosynthetic microbes, including modular cloning, genome editing, and organelle engineering that enable pathway design for lipids, isoprenoids, and proteins. We discuss phototroph-specific bottlenecks for automation and standardization, including slower growth, variable transgene expression, chlorophyll autofluorescence, and the need for controlled illumination and gas exchange with linked data pipelines. Finally, we examine cultivation and scale-up constraints, emphasizing co-optimization of strain traits, reactor design, and downstream processing to improve techno-economic and environmental performance. Photosynthetic biofoundries are therefore both necessary and increasingly feasible for a low-carbon bioeconomy.