Benthic microbial communities (commonly, periphyton) are important components of shallow aquatic ecosystems, occurring as a mixed consortium of algae, bacteria, fungi and detritus associated with benthic substrata. Due to relatively high carbon turnover rates, periphyton can assume a regulatory role in ecosystems, controlling gas and nutrient concentrations, organic and mineral soil accrual, and the quality and abundance of food for aquatic consumers (Stevenson et al. 1996). Periphyton communities also respond very rapidly to environmental changes, driven by rapid cellular responses of competing species that differ in resource use effi ciency, stress resistance, or dispersal capability (Wetzel 2005; Thomas et al. 2006). For this reason, periphyton community attributes are widely incorporated into water quality assessment protocols (Stevenson 1 Department of Biological Sciences, Southeast Environmental Research Center, Florida International University, Miami, FL 33199.