Do Environmental Sequences Clarify the Phylogenetic Relationships and the Geographical Distribution of Ciliates Within the Order Urostylida (Protozoa, Ciliophora)?

As one of the most polymorphic and highly derived ciliate groups, the order Urostylida is a large benthic ciliate group, in which their phylogenetic relationships and geographical distribution remain unclear due to the lack of sufficient data, particularly those difficult to obtain by traditional approach. By using high‐throughput sequencing of the SSU‐rRNA gene V4 region, we obtained 115 OTUs of the subclass Stichotrichia, including 56 OTUs of the order Urostylida, from sediment samples from intertidal flat through continental shelf to deep‐sea habitats including hydrothermal vent, seamount, abyssal plain and Trench with water depth maxing to 6684 m. Compared to the background inferred from phylogenetic analyses based on full‐length SSU‐rRNA gene sequences with detailed morphological identification, the efficacy of using short NGS amplicons in phylogenetic inference has been verified by analysing the ‘clade placement’ and ‘bipartition support’ values. For several taxa in the order Urostylida, our phylogenetic analyses based on short NGS amplicons indicate new clues with higher sensitivity to clarify the phylogenetic relationships. And the present work also provides evidence for marine‐freshwater transitions during the diversification of hypotrichous ciliates. Environment sequences from broader habitats have increased the density of sampling and provided new perspective to understand the phylogenetic and geographical distribution of the benthic ciliate.