The composition of microbial communities within and around plant species is dependent on dynamic physical and chemical signaling events that occur within the local environment and at the root surface.  Visualization and quantification of these events in natural systems is challenging. However, emerging technologies that combine advances in nanostructure fabrication, microfluidics and imaging provide a means of recreating these events within model systems.  These systems mimic aspects of their natural counterparts while providing tractable experimental platforms in which both individual cellular responses and population dynamics can be recorded and analyzed.

Model systems, amenable to imaging, that allow dynamic modulation of local physicochemical cues in a controllable manner have been developed to recreate the interactions between microbes and their hosts.  A nanostructured microfluidic platform has been created in order to examine the chemotactic responses of isolates to specific plant-associated signals.  This platform is created using a combination of electron beam lithography and anisotropic silicon etching techniques.  It can be easily replicated via silicone molding and facilitates the physical tracking of hundreds of microbes within a quasi-two-dimensional space that confines microbes within the focal volume of a conventional phase contrast microscope without significantly impeding natural motility.