Seasonality of planktonic freshwater ciliates with a focus on twelve representatives: Are estimations based on V9 regions of the 18S rRNA gene comparable to classical analyses of morphospecies?. Comparison of classical quantification of ciliates with sequencing analyses

In this study we conducted a three-year sampling campaign in Lake Zurich (Switzerland, n = 74) to create a profound data set for the evaluation and improvement of ciliates specific high throughput sequencing (HTS) data. Two methods, the classical morphotype counting via quantitative silver impregnation (QPS) and Illumina sequencing analyses of the V9 region, were used to investigate the variability in ciliates assemblages over time. To test if the two different approaches resulted in similar outcomes, we focused on seasonal patterns of twelve specific ciliates representatives. These species were isolated from Lake Zurich. Thus their partial 18S rRNA could be sequenced (including the V9 region) after identification and cultivation. With this workflow we gained new sequence information of several key ciliate morphospecies living in freshwater systems.