Molecular diversity and biogeography of benthic ciliates in the Bohai Sea and Yellow Sea

This study explored the molecular diversity and biogeography of benthic ciliates in Chinese marginal seas, the Bohai Sea (BHS), North Yellow Sea (NYS) and South Yellow Sea (SYS). From a previous 18S rRNA gene pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. We found that BHS had the highest ciliate operational taxonomic unit (OTU) richness than NYS and SYS, whereas the richness was not significantly different between summer and winter. Among all the measured environmental variables, water depth showed consistently the strongest correlations with alpha diversities. Overall, the class Spirotrichea (mostly Choreotrichia and unassigned lineages within the class) dominated the communities in terms of both relative proportion of sequences (77.0%) and OTU richness (66.5%). OTU-level ciliate community structure was significant different among the three basins, but not between the seasons. Structurally, significant differences in relative proportion among the basins were detected for the class Litostomatea, but not for other classes. Partial Mantel tests demonstrated that water depth difference was more important than geographic and environment distances in shaping the community structure of benthic ciliates in the studied area. About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described species, indicating a great potential for ciliate species discovery in the offshore sediments. Compared with previous morphology-based surveys, the spatial pattern of ciliate diversity (decreasing from NYS to SYS) is also identified in the present study. Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results (dominance of classes Prostomatea and Karyorelictea in biomass). The potential causes for the discrepancies between molecular and morphological findings are also discussed.