Habitat heterogeneity influences the response of microbial communities to severe low-flow periods in alluvial wetlands

International audience1. Microbial communities play a central role in the functioning of freshwater ecosystems, but the impact of severe low flow on microbial processes at the floodplain scale is largely unexplored, especially in terms of patterns in decline of water level. The differential responses of benthic and interstitial microbial communities are also unknown. 2. We explored the structural and functional responses of bacterial and fungal communities to severe low-flow periods at the surface and deep in the sediment of three types of wetland, namely running water, upwelling zones and isolated pools. 3. The different wetland types exhibited distinct microbial communities but the low-flow period induced homogenisation of community composition among wetland types. Despite a convergence in microbial community composition, the response of microbial processes differed among wetland types during the low-flow period: a decrease in biomass and activity in running water and upwelling sites contrasted with an increase observed in isolated pools. 4. Microbial communities and processes deep in the sediment appeared less affected by the low-flow period and wetland type, but were not insensitive. Homogenisation of community compositions at 50 cm depth was observed 1 month after the low-flow period, suggesting drivers distinct from those at the surface. Our results demonstrate the predominant effect of environmental conditions on rates of microbial processes as opposed to community composition. 5. Wetland heterogeneity, in terms of modalities of water level decrease, seems to be important for the maintenance of microbial processes at the floodplain scale in the context of increasing frequency and severity of low-flow periods