We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contaminationfree recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.two-phase flow | droplet wetting | single-cell analysis | qPCR | environmental genomics M icrofluidic devices provide numerous advantages for biological analysis including automation, enhanced sensitivity and reaction efficiency in small volumes (1, 2), favorable mass transport properties (3, 4), and the potential for scalable and costeffective small volume assays (5). Indeed, advances in microfluidics over the past decade have resulted in increasingly sophisticated functionality and the emergence of two dominant and orthogonal strategies for fluid handling, based either on the use of integrated microvalves or the transport of microdroplets, both in closed channels or over electrode surfaces.The development of soft lithography (6) and the extension of this method to the fabrication of integrated microvalves using multilayer soft lithography (5) has enabled devices with thousands of active microvalves per cm 2 . This high level of integration enables device architectures capable of executing thousands of predefined "unit cell" reactions in parallel, with applications ranging from protein structure (4) and interaction studies (7,8) to single-cell analysis and genomics (2, 9, 10). Two-phase flow systems that manipulate picoliter (pL) volume droplets in closed channels have been shown to be ideally suited to high-speed serial analysis f...