Despite the importance of shallow lakes worldwide, knowledge of microbial components, the base of their food webs, remains scarce. To close this gap, we investigated planktonic microbial food webs, in particular protistan bacterivory (for both ciliates and heterotrophic nanoflagellates [HNF]), in 10 shallow hypertrophic fishponds in South Bohemia (Czech Republic). We used fluorescently labeled bacteria as bacterivory tracers to estimate how abundant protistan populations in fishponds (4–25 × 10³ HNF mL⁻¹ and 55–770 ciliates mL⁻¹) contribute to total bacterial mortality. Fluorescence microscopy, innovative image processing tools, and quantitative protargol staining were combined to detect major bacterivorous and omnivorous ciliate taxa. We quantified bacterial production, bacterivory by individual ciliate species, total ciliates, and total protistan bacterivory in all fishponds. On average, ciliate bacterivory was comparable to that of HNF, accounting for 56% and 44% of total protistan grazing, respectively. We found that primarily bacterivorous Peritrichia (genera Vorticella, Epistylis) and Scuticociliata (Cyclidium spp.) contributed only moderately (mean 26%) to total ciliate bacterivory. Unexpectedly, but highly abundant omnivorous Halteria/Pelagohalteria (Stichotrichia) and, to a lesser extent, also omnivorous Rimostrombidium spp. (Oligotrichia) contributed significantly more (mean 71%) to total ciliate bacterivory than typical bacterivorous taxa. This suggests that unselective grazers, which feed on a broader size spectrum from bacteria to small algae, may have a considerable competitive advantage in hypertrophic environments rich in small particles. Moreover, a meta‐analysis of available literature data supports our hypothesis that the role of ciliate bacterivory increases significantly, relative to HNF bacterivory, along a trophic gradient toward hypertrophic habitats.

Important drivers of gross primary production (GPP) and ecosystem respiration (ER) in lakes are temperature, nutrients, and light availability, which are predicted to be affected by climate change. Little is known about how these three factors jointly influence shallow lakes metabolism and metabolic status as net heterotrophic or autotrophic. We conducted a pan‐European standardized mesocosm experiment covering a temperature gradient from Sweden to Greece to test the differential temperature sensitivity of GPP and ER at two nutrient levels (mesotrophic or eutrophic) crossed with two water levels (1 m and 2 m) to simulate different light regimes. The findings from our experiment were compared with predictions made according the metabolic theory of ecology (MTE). GPP and ER were significantly higher in eutrophic mesocosms than in mesotrophic ones, and in shallow mesocosms compared to deep ones, while nutrient status and depth did not interact. The estimated temperature gains for ER of ~ 0.62 eV were comparable with those predicted by MTE. Temperature sensitivity for GPP was slightly higher than expected ~ 0.54 eV, but when corrected for daylight length, it was more consistent with predictions from MTE ~ 0.31 eV. The threshold temperature for the switch from autotrophy to heterotrophy was lower under mesotrophic (~ 11°C) than eutrophic conditions (~ 20°C). Therefore, despite a lack of significant temperature‐treatment interactions in driving metabolism, the mesocosm's nutrient level proved to be crucial for how much warming a system can tolerate before it switches from net autotrophy to net heterotrophy.