Seasonal variation of the protist assemblage in the Columbia River coastal margin assessed using 18S rRNA gene sequences

Sequence analysis of the 18S (SSU) rRNA gene was undertaken to assess the seasonal dynamics of the protist assemblage across a salinity gradient encompassing the Columbia River (0 PSU), estuary (15 PSU) and plume (28-31 PSU) during the spring and summer months of 2007 and 2008. Microscopic examination of the larger protists (diatoms and dinoflagellates) showed good agreement with the sequence analysis at the taxonomic level of class (86% similar according to the Bray-Curtis similarity metric), but the two methods diverged at the genus level (40% similar). Bacillariophyceae (diatoms) was the most numerous protist class in the 0 PSU and plume waters in the spring and early summer (April 2007, April 2008, and July 2008). However, members of the genus Katablepharis, a 5 μm heterotrophic flagellate, were the prevalent protists within the estuary in April 2007 and 2008 based on the number of retrieved sequences. Through SSU sequence analysis we detected a shift from diatoms to motile protists, including dinoflagellates and the ciliate, Myrionecta rubra, in the estuary and plume between the spring/early summer and late summer in both years. Nitrate concentration explained most of the seasonal variability in the protist assemblage, while salinity was the major influence on assemblage variability across the river-to-ocean gradient.