Terminal-restriction fragment length polymorphism (T-RFLP) is a DNA-based technique used to examine microbial community structure. We used this technique to examine variability in microbial community structure in 3 pools and a riffle in a semipermanent stream that becomes a chain of pools during the summer. We examined microbial communities under 3 hydrological conditions: predrought (all sites inundated), drought (all sediments dried for ≥2 mo), and rewet (1 mo after inundation). We used nonmetric multidimensional scaling to ordinate microbial communities and analysis of similarity to test whether communities differed among sites and whether community structure within sites changed in response to drought and rewetting. Microbial communities within sites differed with respect to hydrological condition, with most within-site variability occurring within the riffle section of the stream. Sediment drying significantly changed the microbial community structure at all sites. One month after rewetting at all sites, the microbial communities had not returned to their predrought structures and were significantly different from the predrought and drought microbial communities. Within-site variability in microbial community structure was much lower after the drought than before the drought. T-RFLP proved to be a powerful method for resolving microbial community structure, and its application helped address our limited understanding of microbial community dynamics.
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