Microfluidic automation technology for synthetic biology offers significant opportunities for the development of life sustaining biological systems for long term space exploration missions. Among the potential applications are enhanced production of food and fuels from photosynthetic organisms, processing of waste products such as CO2 or urea, atmosphere regeneration, and water re-utilization as a part of environmental control and life support on the International Space Station. By engineering with new or enhanced metabolic pathways for the production or processing of chemical resources or waste, photosynthesis using cyanobacteria can be a particularly effective mechanism for environmental control and life support. Synthetic biology offers significant advancements in a broad range of commercial applications including biofuel production, drug development, and agricultural development. The utility of our microfluidic technology in diverse fields is further enhanced by the development of automation procedures for a suite of organisms including cyanobacteria, E. coli, and yeast. As such, the proposed technology could be used in engineering biological processes such as mass producing effective medications, manufacturing specialty chemicals, engineering organisms and enzymes for better biofuel production, or developing crops that are more resistant to pathogens or drought. Generating and screening multiple combinations of genes, enzymes, and other biological parts is also vital to biotechnology research and development.