Protist diversity and community structure across temperate European estuaries: insights from environmental DNA metabarcoding.
The environmental gradients in the dynamic transition zones of estuaries significantly determine microbial life.  Broad patterns in the diversity and composition of eukaryotic protist communities were studied in three contrasting estuaries of the Gulf of Cádiz (Guadalquivir, Guadiana, and Tinto–Odiel) using environmental DNA (eDNA) metabarcoding of the 18S rRNA gene. Throughout the three systems, protist communities were dominated by the major eukaryotic supergroups comprised of Stramenopiles, Alveolata, and Rhizaria, but their relative contributions differed markedly among the estuaries. The structure of communities followed clear environmental gradients, the main factors associated with taxonomic composition, dominance, and evenness were salinity and redox conditions. The estuaries characterized by stronger marine influence supported more homogeneous communities where only a few taxa dominated, whereas those with a higher hydrodynamic variability demonstrated a greater taxonomic heterogeneity and with a lower dominance of any particular taxon. These results reveal consistent ecological patterns protist assemblages found in estuaries and clearly indicate the sensitivity of microbial eukaryotes to changes in physical and biogeochemical conditions. This study demonstrates the value of eDNA metabarcoding when identifying large-scale biodiversity patterns in estuarine ecosystems and justifies its application when monitoring coastal environments exposed to natural and anthropogenic pressures.