Diversity and changes in seasonal abundances of marine ciliates in the Southern California Bight

Traditional methods of measuring ciliate abundances are tedious and require expert identification of cells through microscopy. A high-throughput molecular assay was used in this study to assess relative abundances of marine ciliates in a time-series from the SIO Pier, La Jolla, CA that would be difficult to obtain by traditional methods. Using ciliate-specific primers, 18S environmental clone libraries from the waters of La Jolla and Point Conception, CA were created to determine the diversity of ciliates. Four Eutintinnus sp. and two Strombidium sp. nucleotide probes were designed from the sequences obtained. These probes, with a high throughput bead hybridization (Luminex), were used to analyze seasonal changes in abundances from January 2005 to January 2008. Peak abundances occurred in the spring for probes Eut 1, Eut 2A and Eut 3A and in the summer for probes Eut 4, Str 1 and Str 2. Spring and summer abundances were also seen in previous numerical cell counts (Beers and Stewart 1970). No correlation was found between ciliate abundances and previously reported Synechococcus numbers (Tai and Palenik 2009). Half of the species probes, Eut 2A, Eut 3A and Str 1, had a negative correlation to chl and two, Eut 4 and Str 2 correlated positively with temperature and salinity. This new method has great potential for further studies of ciliate ecolog