1) planktonic eukaryotic community; 2) surface water collected from Pearl River Estuary, South China Raw sequence reads. aquatic metagenome

The microeukaryotic plankton diversity and composition impact on environmental restoration and ecological processes in estuarine ecosystem; therefore, investigating the factors that influence microeukaryotic plankton biodiversity is critical to addressing urgent questions related to environmental pollution and ecological deterioration. In this study, we assessed the diversity and distribution of eukaryotic microbial community in 24 water samples collected from eight major outlets in Pearl River, South China, by using Illumina Hiseq sequencing targeting the 18S rRNA V9 region.