Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.

雨林水生生态系统包括复杂的栖息地，关于其单细胞真核生物多样性和群落结构的信息很少。我们基于通过高通量 DNA 测序获得的 18S-rDNA 的高变 V4 区域，研究了巴西大西洋森林沿岸淡水和咸水环境中纤毛虫的多样性。我们的分析检测到 409 个纤毛虫分类单位 (OTU)，主要归因于寡膜虫纲和螺旋体纲。共报告11纲、12亚纲、112属、144种。我们发现以下几点：(a) 淡水中的纤毛虫群落比大西洋森林相关的咸水环境更加多样化；(b) 纤毛虫群落由少量的高丰度 OTUs 和大量低丰度或稀有 OTUs 组成；(c) 近三分之一的纤毛虫 OTU 与参考序列的序列同一性低于 97%，并且 (d) 系统发育推断支持了纤毛虫 18S-rDNA 的 V4 区域是在类中进行准确进化推断的合适标记的假设等级。我们的结果表明，在目前可用的分子数据库中没有代表来自巴西大西洋森林的 HTS 检测到的纤毛虫多样性的相当一部分。