Hydrological variability and connectivity shape floodplain microbial community dynamics

Abstract Floodplains are dynamic interfaces between aquatic and terrestrial ecosystems, where ecosystem functioning is strongly influenced by microbial communities. To investigate the composition of free‐living and particle‐associated prokaryotic and microbial eukaryotic communities, five interconnected study sites were sampled in one of the best‐preserved Danube floodplains and subsequently analyzed using 16S and 18S rRNA gene amplicon sequencing. We compared community dynamics across low‐water periods and minor to moderate floods and observed flooding to increase microbial diversity and promote gradual community shifts depending on flood intensity, whereas low‐water conditions limited microbial exchange and reduced compositional connectivity across floodplain ecosystems. Dispersal effects were particularly pronounced in microbial eukaryotes, including Perkinsea and Fungi, pointing to the importance of hydrological connectivity in structuring micro‐eukaryotic communities. Flooding also facilitated community mixing and more balanced interspecific interactions, while low‐water periods led to more compartmentalized networks. Core microbial community size increased with flooding intensity, reflecting the influence of ecosystem mixing, allochthonous inputs, and increased nutrient availability in shaping floodplain communities. This study highlights the effects of flooding intensity on both prokaryotic and microbial eukaryotic communities, advancing our understanding of how hydrological variability shapes microbial dynamics in riverine floodplains.