Freshwater Discharge and Salinity Drive Taxonomic and Functional Turnover of Microbial Communities in a Turbid Macrotidal Estuary

The drivers of spatiotemporal changes in microorganism's functional community structure remain poorly understood. Using DNA-amplicon sequencing we studied the spatiotemporal dynamics of bacterial and eukaryotic microbial communities in the freshwater and brackish tidal reaches of the Schelde estuary (Belgium) from 2018 to 2021. Our analyses revealed pronounced seasonal and longitudinal turnover in autotrophic and heterotrophic microbiota, mainly driven by changes in freshwater discharge, which modulate the salinity and turbidity gradient. Higher discharge in early spring led to a more uniform community composition across the estuary, with higher relative abundances of heterotrophic eukaryotes. As discharge decreased in late spring, the salinity gradient and associated turnover in community composition became more accentuated, with Actinomycetota and diatoms dominating the upstream reaches, and ciliates, fungi and marine bacteria being relatively more important downstream from the maximum turbidity zone (MTZ). This study revealed fine-scale turnover in (semi)cryptic phytoplankton taxa and spatiotemporal changes in parasitism linked to bloom termination. High discharge due to exceptionally heavy rainfall resulted in the disruption of the phytoplankton bloom, more downstream spreading of freshwater species and a decline in brackish and polyhaline species. These results emphasise the intricate link between hydrodynamics and microbial community dynamics and ecological functions in estuarine ecosystems.