Prokaryotic communities in riverbed sediments of an intermittent stream

We performed a microcosm-based experiment to investigate how dry period duration (0, 3, 6 and 9 weeks) and magnitude of rewetting by rainfall (0, 4 and 21mm) affected the nitrogen (N) content, nitrifying microbial communities, ammonia oxidation (AO) rates, and nitrous oxide (N2O) fluxes in riverbed sediments. Ammonium (NH4+) decreased whereas nitrate (NO3-) increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of some nitrifiying microbial groups (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes, respectively) increased, despite the decrease in measured AO rates over drying. An increase of N2O emissions occurred at early drying, but then fluxes substantially dropped until the end of the experiment. Rainfall of 21 mm increased AO rates and NH4+ in sediments, whereas rainfall of 4 mm triggered N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Consequently, alternating dry-wet scenarios in rivers, predicted to grow more influential in the future, can play a fundamental role in N processing and transport along fluvial networks.