The familar view of microbes in their free (planktonic) state is not the norm; rather it is believed that much of the microbial biomass, perhaps 95-99%, is located in close-knit communities, designated biofilms and microbial mats, consisting of large numbers of organisms living within self-secreted matrices constructed of polymers and other molecules. (Microbes in collective behave very differently from their planktonic state; even genetic expression patterns change.) These matrices serve the purposes of anchoring and protecting their communities in favorable locations while providing a framework in which structured populations can differentiate and self-organize.
  One of the salient features of biofilms is their spatial heterogeneity; they are not uniform, well-mixed systems like many laboratory microbial communities are. Because of spatial variation, advective and diffusive processes become influential, greatly increasing the complexity of these systems. We will discuss implications through a number of ecological and physical examples.