Diversity Patterns of Protists are Highly Affected by Methods Disentangling Inter-specific Variants: A Case Study in Oligotrich (s.l.) Ciliates

An enormous amount of environmental sequences produced by high-throughput sequencing (HTS) is popular for inferring diversity and distribution patterns of protists, which are widely distributed and playing important roles in energy flux and nutrient cycling. However, study testing whether methods disentangling inter-specific variants affect the diversity and distribution patterns of protists using field samples is insufficient. Using oligotrich (s.l.) ciliates, one group of abundant and dominate planktonic protists, in field samples as an example, the present study indicates that DADA2 performs better than UCLUST and UPARSE for inferring diversity patterns of oligotrich (s.l.) ciliates in Pearl River Estuary and surrounding regions. UPARSE, as an OTU-construction method might underestimate species richness and produce less reliable beta diversity pattern than DADA2. UCLUST with 97% and 99% clustering thresholds overestimate species richness, and the beta diversity pattern inferred by the former one is unreasonable. Salinity is shown to be one of the key factors responsible for variations in community distribution of ciliates, but infrequent marine-freshwater transitions occurred during evolutionary terms of this group.