Resumen
Ciliates are fundamental components of microzooplankton, with important ecological roles. However, ciliate communities are particularly difficult to monitor using conventional morphological approaches. New molecular tools, such as DNA metabarcoding, can facilitate the study of these communities. This study used high-throughput sequencing to examine the diversity and seasonal dynamics of ciliate communities in four estuarine ecosystems in the South China Sea from June 2019 to March 2020. The amplification of the V4 region of 18S rDNA using ciliate-specific primers identified a total of 1645 amplicon sequence variants (ASVs), corresponding to 13 ciliate classes, 97 families, and 157 genera. The dominant species across all four sampling stations were spirotrichs (including choreotrichs, oligotrichs, and stichotrichs), oligohymenophorean scuticociliates, litostomateans Didinium, and prostomateans Cryptocaryon. Significant differences in ciliate diversity and community composition in the four stations were mainly due to differences in rare, rather than abundant, ASVs. Analysis of the ciliate communities and seasonal patterns in their composition revealed that variations in habitat and environmental conditions have a greater effect than seasonal changes on community composition.