Estuaries are complex ecosystems that connect riverine and marine environments, where microorganisms play a key role in maintaining ecosystem functions. In this study, we investigated the dynamics of bacterial and eukaryotic communities in the Seine estuary (Normandy, France) over the course of one year, across eight sites, at two depths, with monthly sampling. To date, the taxonomy of the microbial diversity present in this anthropized estuary remains poorly understood, and the factors influencing the structure of microbial communities have yet to be identified.
Metabarcoding analysis of 147 samples revealed high bacterial and eukaryotic diversity, dominated respectively by Proteobacteria, Bacteroidota, Actinobacteriota, and Bacillariophyta, Spirotrichea, Dinophyceae. Along the estuary, we observed significant variations in bacterial and eukaryotic community composition during only three and two months out of twelve, respectively. However, a marked seasonal effect was observed on the diversity of both microbial communities, influenced by fluctuating physico-chemical variables throughout the year (temperature, irradiance, river discharge). Biotic interactions also proved to be key factors influencing alpha and beta diversity. Throughout the year, we identified a diverse and abundant core microbiome, composed of 74 bacterial OTUs and 41 eukaryotic OTUs. These regionally abundant species include habitat generalists encompassing heterotrophs, phototrophs, and consumers. However, a large portion of these core OTUs remains poorly assigned both taxonomically and functionally.
This molecular study represents a key step in understanding the dynamics of macrotidal estuaries and the Seine ecosystem, by identifying potential markers of ecosystem functions. It also highlights the importance of seasons and biotic associations as major drivers structuring the microbiome of the Seine estuary, as well as the presence of a persistent core microbiome throughout the year.
