The abundance and biomass of surface (5 m) and deep (30–45 m) ciliate and dinoflagellate protozoa in the offshore waters of Lakes Huron and Michigan were determined from December 1986 to November 1987. Protozoan (ciliates and dinoflagellates) abundance (4 to 15 cells·mL −1) and biomass (13–140 μg·L −1, wet wt.) were comparable between lakes and similar to those reported from other oligotrophic environments. On average, ciliates comprised the majority of protozoan abundance (80%) and biomass (73%). The mean size (ESD) of these communities was small (20.6 μm) due to the numerical dominance of small choreotrichs, oligotrichs, and species of Gymnodinium. Total biomass in both lakes peaked during late June-July and again during the October-November period. These seasonal changes in biomass were accompanied by species replacements: tintinnids, strobilids, oligotrichs, and Gymnodinium species were abundant in the spring isothermal period, shifting to oligotrich dominance during summer stratification (May–July); a more diverse assemblage followed during late stratification (October–November) in which haptorids, prorodontids, and Peridinium species became more important. Deep and surface communities were comparable in terms of abundance and biomass, although deep community biomass decreased as stratification intensified. Because the biomass of ciliates alone represents approximately 30% of crustacean zooplankton biomass, protozoa may be more important grazers than once thought.
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