Community composition patterns of benthic protists were investigated in salinity-disparate lakes, including a coastal saline lake (Lake Hiruga), a brackish lake (Lake Suigetsu) and a freshwater lake (Lake Biwa). Samples were collected from the surface layer of anoxic sediment (0–5 cm depth horizon) at each lake; two sets of samples were collected 2 months apart. Sequences of 18S rRNA genes were analysed using high throughput sequencing. We obtained 63,619–389,041 sequences per sample, resulting in 4,331 operational taxonomic units (OTUs) based on 98% similarity. Cluster analysis showed that the community structures between seasons in each lake were similar, while there were marked differences among lakes. Other than photosynthetic organisms, Metazoa and Fungi, 3,018 (70%), 1,132 (26%) and 391 (9%) of protistan OTUs were obtained from lakes Biwa, Hiruga and Suigetsu, respectively. Taxonomic analysis showed 23 OTUs (5.3%) were common to the three lakes, and were composed of 19 Alveolata-, three Stramenopiles- and one unclassified-related taxa. Our results suggest that salinity is an important environmental variable that determines community composition of protists in anoxic sediments in lakes.
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