Composition, Distribution, and Assembly Patterns of Eukaryotic Communities under Vertical Geochemical Gradients in a Polluted Urban River

Eukaryotes are critical regulators of ecosystem functions in river systems. However, little is known about vertical micro-eukaryotic composition, diversity, and assembly patterns in urban aquaculture systems under vertical geochemical gradients. Molecular analysis based on 18S rRNA gene sequencing was performed to investigate the spatial variation in the eukaryotic community in six layers of different depths in water and sediments in the Jinchuan River of Nanjing, China. SAR and Opisthokonta were the most abundant groups, comprising 75.19% and 10.54% of the total sequences in water and 32.43% and 44.10% of the total sequences in sediment, respectively. The composition, diversity, and assembly patterns of eukaryotic microbes varied regionally and spatially in different layers. The abundance of Paramecium increased, and that of Ploimida decreased as the level of water pollution increased in water layers. In sediment layers, Cyclotella, Ochromonas, and Stentor were more abundant in less-polluted sites. In addition, depth-related differences could also be observed among eukaryotes in different layers. Paramecium was most common across all water layers with an average relative abundance of 19.64%, while LKM11 dominated the community in sediment (18.79%). Statistics of the beta-diversity patterns suggested that a higher level of river pollution probably leads to greater heterogeneity in eukaryotic community composition (BSOR-C > BSOR-A > BSOR-D > BSOR-B). Vertical beta-diversity patterns in the eukaryotic community primarily resulted from species replacement, which was mainly driven by spatial turnover (βSIM = 0.4471 in water and 0.6662 in sediment) rather than nestedness (βNES = 0.0292 in water and 0.0188 in sediment).