Abstract: The present invention is directed to the application of robotics to screen and optimize microorganisms for their bioremediation capabilities. In particular, the present invention provides methods to screen for the ability of microorganisms to metabolize particular compounds of interest in bioremediation applications. The present invention also provides a method for discovery of microorganisms useful for bioremediation and biomining, as well as other applications where microbial metabolism is useful for catalyzing chemical biotransformations.