Culture-independent assessment of planktonic ciliate diversity in coastal northwest Atlantic waters

Planktonic ciliates within the subclasses Choreotrichia and Oligotrichia play critical roles in food webs in the world's oceans. To assess the diversity of these ciliates, we designed primers specific to small subunit ribosomal DNA (SSU rDNA) of ciliates within these clades and sampled at 3 coastal sites in the northwest Atlantic in October 2004 and May 2005. We also preserved and analyzed samples using standard ecological methods to compare observations from light microscopy with our molecular results. We found that (1) estimates of diversity based on molecular markers were similar to estimates from morphological observations for choreotrich ciliates, but much greater for oligotrich ciliates; (2) while similar levels of diversity were found at each site, each collection had its own distinct assemblage of rare and abundant ciliate haplotypes; (3) genealogical analyses of our samples combined with published sequences from identified morphospecies revealed that haplotype diversity at these sites is greatest within the genus Strombidium, in the Oligotrichia. The results from this ciliate-specific analysis are consistent with previous molecular studies on microbial diversity in marine systems in that they reveal high diversity and shifting assemblages within microbial communities.