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Bottom-up approach in understanding and developing gene networks calls for study of cells on a single cell level. Microfluidic technology provides such necessary tools to examine single cells not only in static but even more importantly in dynamic environments. Here we present studies that focus on examining model organisms of Escherichia coli and Saccharomyces cerevisiae on single cell and colony level. First, we developed a microfluidic device for studying single cell response of Galactose network of S. cerevisiae in fluctuating carbon source environment. As part of the study we have developed a novel off-chip technology that allows for fast and dynamic control of extracellular environment. In addition, this microfluidic device allows for 8 independent single cell level experiments to be run simultaneously. Next, this technology was adapted to study protein expression on single-protein level in E. coli. Furthermore, we developed a microfluidic device to study and characterize a colony- coupled synthetic oscillator in E. coli. To study the diffusion characteristics of the coupling agent the scale of the devices was increased from nominal 100,000 cells to include over 50 million cells. Lastly, we combined the ability to generate a dynamic environment with a large- scale device to study long-term population dynamics of two competing S. cerevisiae strains