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Calanoid copepods, rather than cladocerans, frequently dominate the zooplankton of lakes in New Zealand. The potential consequences of this domination for the microbial community of mesotrophic Lake Mahinerangi, New Zealand, were determined by field experiments in which  Boeckella  and  Daphnia  were added to  in situ  enclosures in the presence and absence of added nutrients. Boeckella hamata at ambient densities (2 and 81 −1 ) rapidly and severely suppressed ciliate population growth over 4 days, even when microbial growth was enhanced by added nutrients, but effects of copepods on other components of the microbial community (bacteria, photosynthetic picoplankton, heterotrophic nano-flagellates, algae) were slight. In contrast,  Daphnia carinata  at the same densities (but 3-fold higher biomasses per litre) had a relatively weak effect on ciliates, suppressing ciliate abundance only after 4 days at 8  Daphnia  1 −1  (330 μg 1 −1 ); this daphniid density also depressed abundances of large bacterial rods, some photosynthetic picoplankton and the dominant alga,  Cyclotella . These results highlight the relative importance of specific trophic linkages in a microbial food web; they also suggest that the dominance of  Boeckella  in many southern hemisphere lakes may account for relatively low ciliate abundances in these lakes.

Relative impacts of copepods, cladocerans and nutrients on the microbial food web of a mesotrophic lake