Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and DGGE in temperate coastal waters

We assessed the diversity of coastal planktonic ciliates (Oligotrichia and Choreotrichia, Class: Spirotrichea) in Fishers Island Sound off the coast of Connecticut, USA using a combination of denaturant gradient gel electrophoresis (DGGE) and morphological analyses. To test the hypothesis that ciliate communities followed water masses, we sampled 3 times at a surface drifter (i.e. floating buoy) and twice at intervening times from points 1 km away. By repeating both PCRs and gel electrophoresis under varying conditions, we confirmed that DGGE is an appropriate tool to capture the ciliate community composition, based on the high repeatability of samples. The 2 methods used for assessing ciliate community structure showed similar levels of diversity for tintinnids. However, there was a mismatch in diversity estimates for the aloricate ciliates, especially for the oligotrichs where the estimated diversity was greater by DGGE than by microscopy. This may be attributable to biases in the DGGE (e.g. primer or gene copy number issues) and/or misidentification by morphology. However, the pattern of community structure assessed by cluster analyses is similar for both microscopy and DGGE, suggesting that the mismatch between these methods does not introduce bias in biogeographical analysis. Analyses of both DGGE haplotypes and microscopically observed morphospecies revealed that the ciliate communities were not static within the water mass. Community structure and abundance patterns varied with salinity and currents. These changes could be due to mixing with adjacent estuarine and coastal assemblages, ciliate behavior, and/or other factors that cause assemblages to be dynamic over short (i.e. ultradian) periods.