The abundance, biomass and composition of planktonic ciliates were studied in two Great Lakes of Africa, Malawi and Victoria, between June, 1997, and June, 1999, to investigate their role in the food webs of these lakes. Oligotrichs (Strombidium , Strobilidium and Halteria) were the most abundant group of ciliates in both lakes. Other important ciliates in terms of abundance and/or biomass included heterotrichs, peritrichs, haptorids, and peniculids. Mean ciliate abundance was 1.5 ciliates · mL−1 and 20.1 ciliates · mL−1 in Lakes Malawi and Victoria, respectively. Ciliate biomass ranged from 0.03 to 7.82 μg C · L−1 (mean 1.8 ± 0.7 μg C · L−1) in Lake Malawi and ranged from 24.2 to 61.82 μg C · L−1 (mean 36 μg C · L−1) in Lake Victoria. Ciliate abundance and biomass were higher at offshore than inshore stations of both lakes despite that chlorophyll exhibited the opposite trend. Both lakes demonstrated vertical and temporal variation in their ciliate communities as well. Herbivores were an important feeding guild in both lakes, while mixotrophs and bacterivores were also important in Lakes Malawi and Victoria, respectively.

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