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.

Summary 1. We followed microbial and other planktonic communities during a 4‐month period (February–May) in 12 outdoor flow‐through mesocosms designed to elucidate the effect of global warming and nutrient enrichment. The mesocosms were established in 2003. 2. Warming had a smaller effect than nutrients on the biomass of the microbial and planktonic communities, and warming and nutrients together exhibited complex interactions. 3. We did not find direct effects of warming on the biomass of bacterioplankton or ciliates; however, warming significantly added to the positive effect of nutrients on these organisms and on heterotrophic nanoflagellates (HNF). No warming effects on any of the other planktonic groups analysed were detected. 4. The zooplankton: phytoplankton biomass ratio was lowest, and the HNF: bacteria and rotifer: bacteria biomass ratios highest in the heated, nutrient‐rich mesocosms. We attribute this to higher fish predation on large‐bodied zooplankton, releasing the predation on HNF and competition for rotifers. 5. The proportion of phytoplankton to the total plankton biomass increased with nutrients, but decreased with warming. The opposite pattern was observed for the proportion of phytoplankton to the total microbial biomass. 6. As climate warming may lead to eutrophication, major changes may occur in the pelagic food web and the microbial community due to changes in trophic state and in combination with warming.

Climate change is expected to profoundly affect both temperature and net precipitation, with implications for lake water level. We describe the design of a harmonized, simultaneous, cross-European mesocosm experiment to elucidate the effects of climate change on community structure, functioning, and metabolism in shallow lakes at low and high nutrient levels with contrasting depths (1 and 2 m). We used cylindrical (D = 1.2 m) tanks that were either 1.2 or 2.2 m high, each having a 10-cm sediment layer. We inoculated the mesocosms with a mixed sample of sediment and plankton from lakes with contrasting nutrient concentrations and added macrophytes and planktivorous fish. Sediment was pre-equilibrated to the required experimental nutrient concentration. During the experiment the water level decreased with increasing temperature (up to 90 cm in the Mediterranean mesocosms) while conductivity increased. The average chlorophyll a concentration increased with temperature in the deep mesocosms but was more variable in the shallow mesocosms. Macrophyte F. Landkildehus et al. 72abundance increased with temperature, while the oxygen data suggest that net primary production peaked at intermediate temperatures. We conclude that our experimental design has the potential for tracking the interacting effects of global warming and eutrophication in shallow lakes.

Summary The response of planktonic (phytoplankton, ciliates, rotifers and crustaceans) and littoral (Ephemeroptera, Plecoptera, Trichoptera and Heteroptera: Nepomorpha) assemblages to chemical recovery was studied over a twelve‐year period (1999–2011) in eight glacial lakes in the Bohemian Forest (central Europe). The region suffered from high atmospheric pollution from the 1950s to the late 1980s, but has since been recovering from acidification due to 86% and 44% decrease in sulphur and nitrogen deposition, respectively, during the 1990s–2000s. Despite the rapid improvement in water chemistry of all the eight studied lakes, only four have partly recovered so far (low‐aluminium lakes), while the other four lakes still remain strongly acidic (high‐aluminium lakes). All present lake assemblages are dissimilar by 40–90% from those during the early phase of chemical recovery as a result of species (re)colonisation (ciliates, crustaceans and insects) in the high‐Al lakes, and considerable species replacement (zooplankton) and (re)colonisation (insects) in the low‐Al lakes. Phytoplankton remained very similar in the high‐Al lakes, but changed (loss and/or replacement of some acid‐tolerant species) in the low‐Al lakes. Aluminium (Al) concentrations were dominant in structuring the assemblages of phytoplankton, rotifers and Nepomorpha, but also affected crustaceans through the seston carbon to phosphorus (P) ratio. Both direct (toxicity) and indirect (P availability) effects of Al control biological recovery in the Bohemian Forest lakes. A concentration of 200 μg L−1 of total Al is the main barrier preventing the high‐Al lakes from recovery. In contrast, pH and total P rather than Al significantly influenced Ephemeroptera, Plecoptera and Trichoptera. Although biotic responses (especially in the low‐Al lakes) showed important signs of recovery, such as reappearance of some indigenous or acid‐sensitive species, decline in eurytopic acid‐tolerant species and colonisation by vagile species, the assemblages of all the lakes still suffer from acid stress. Our results also indicate an increasing role of biotic interactions between colonisers and residents leading to the reconstruction of aquatic food webs in the low‐Al lakes.

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