Non-perennial systems experience repeated drying-rewetting cycles, which regulate microbial activity and nutrient processing, yet the functional consequences of dynamic flow patterns remain poorly resolved. To understand the effects of variable surface water flow on lotic microbial communities, we conducted a flow manipulation experiment on Shane’s Creek at the Konza Prairie Biological Station in northeastern KS, USA, and conducted continued sampling through a natural dry-down period. We evaluated how microbial populations and decomposition enzyme activities in contrasting microhabitats (benthic sediment vs. epilithon) and geomorphological features (pool vs. riffle) responded to flow alteration. We quantified sediment and epilithon DNA concentrations, bacterial and fungal populations, extracellular enzyme activities (EEA, β-glucosidase (BG), N-acetylglucosaminidase (NAG), and alkaline phosphatase (AP)) across high-flow, drying, dry, and rewetting timepoints. We predicted that population size and enzyme production would increase with hydrologic connectivity due to higher nutrient delivery, with habitat-specific differences such as increased sensitivity to drying in epilithic biofilms and greater resistance to drying in sediment habitats.
Changes in surface water flow affected decomposition enzyme activities differentially among habitats. In riffles, epilithon NAG activity increased upon rewetting (p = 0.001), while sediment NAG activity increased during drying but decreased following rewetting (p < 0.001). In pools, sediment NAG activity was comparatively stable through changing flows (p = 0.012). BG and AP in sediments and epilithon also differed consistently between pools and riffles (p < 0.03). All BG:NAG activity ratios declined during the natural dry-down, indicating increasing N limitation, but showed no flow manipulation response. DNA yield, a proxy for microbial biomass, was more stable in epilithon than sediments, in that riffle DNA yield was low during high-flow periods, and increased during the natural drying period (p < 0.001). Thus, results fit our predictions, though with greater sensitivity in riffle sediments than expected. Collectively, the study demonstrates how drying-rewetting cycles affect microbiota in a non-perennial stream, with epilithon function and riffle sediment biomass exhibiting heightened sensitivity to dynamic surface flows. Further analysis of integrated decomposition rates and fungal and bacterial gene diversity will be used to assess microbial composition and function in response to flow modifications.