Eukaryotic phytoplankton form the basis of aquatic food webs and play a key role in the global carbon cycle. Many of these evolutionarily diverse microalgae are also capable of feeding on other microbes, and hence simultaneously act both as primary producers and consumers. The net ecosystem impact of such mixotrophs depends on their nutritional strategy which is likely to alter with environmental change. Many temperate lakes are currently warming at unprecedented rates and are simultaneously increasing in water color (browning) due to increased run‐off of humic substances. We hypothesized that the resulting reduction in light intensity and increased bacterial abundances would favor mixotrophic phytoplankton over obligate autotrophs, while higher temperatures might boost their rates of bacterivory. We tested these hypotheses in a mesocosm experiment simulating a gradient of increasing temperature and water color in temperate shallow lakes as expected to occur over the coming century. Mixotrophs showed a faster increase in abundance under the climate change scenario during spring, when they dominated the phytoplankton community. Furthermore, both bacterial abundances and rates of phytoplankton bacterivory increased under future climate conditions. Bacterivory contributed significantly to phytoplankton resource acquisition under future climate conditions, while remaining negligible throughout most of the season in treatments resembling today's conditions. Hence, to our knowledge, we here provide the first evidence for an increasing importance of bacterivory by phytoplankton in future temperate shallow lakes. Such a change in phytoplankton nutritional strategies will likely impact biogeochemical cycles and highlights the need to conceptually integrate mixotrophy into current ecosystem models.

Extreme climatic events, such as heat waves, are predicted to increase in frequency and intensity during the next hundred years, which may accelerate shifts in hydrological regimes and submerged macrophyte composition in freshwater ecosystems. Since macrophytes are profound components of aquatic systems, predicting their response to extreme climatic events is crucial for implementation of climate change adaptation strategies. We therefore performed an experiment in 24 outdoor enclosures (400 L) separating the impact of a 4 °C increase in mean temperature with the same increase, that is the same total amount of energy input, but resembling a climate scenario with extreme variability, oscillating between 0 °C and 8 °C above present conditions. We show that at the moderate nutrient conditions provided in our study, neither an increase in mean temperature nor heat waves lead to a shift from a plant-dominated to an algal-dominated system. Instead, we show that species-specific responses to climate change among submerged macrophytes may critically influence species composition and thereby ecosystem functioning. Our results also imply that more fluctuating temperatures affect the number of flowers produced per plant leading to less sexual reproduction. Our findings therefore suggest that predicted alterations in climate regimes may influence both plant interactions and reproductive strategies, which have the potential to inflict changes in biodiversity, community structure and ecosystem functioning.

A major challenge for ecological research is to identify ways to improve resilience to climate-induced changes in order to secure the ecosystem functions of natural systems, as well as ecosystem services for human welfare. With respect to aquatic ecosystems, interactions between climate warming and the elevated runoff of humic substances (brownification) may strongly affect ecosystem functions and services. However, we hitherto lack the adaptive management tools needed to counteract such global-scale effects on freshwater ecosystems. Here we show, both experimentally and using monitoring data, that predicted climatic warming and brownification will reduce freshwater quality by exacerbating cyanobacterial growth and toxin levels. Furthermore, in a model based on long-term data from a natural system, we demonstrate that food web management has the potential to increase the resilience of freshwater systems against the growth of harmful cyanobacteria, and thereby that local efforts offer an opportunity to secure our water resources against some of the negative impacts of climate warming and brownification. This allows for novel policy action at a local scale to counteract effects of global-scale environmental change, thereby providing a buffer period and a safer operating space until climate mitigation strategies are effectively established.

Summary Cyanobacterial blooms are a worldwide phenomenon in both marine and freshwater ecosystems and are predicted to occur more frequently due to global climate change. However, our future water resources may also simultaneously suffer from other environmental threats such as elevated amounts of humic content and consequent increased water colour, a phenomenon called ‘brownification’. In order to investigate the effects of temperature and water colour in combination, we performed a mesocosm experiment combining a 3 °C increase in temperature and a doubling in water colour. With this, we created a projected future scenario for our water resources, and we specifically focused on how these changes would affect cyanobacterial bloom formation and toxicity. We showed that despite total cyanobacterial biomass remaining unaffected, the abundance of one individual cyanobacterial species, Microcystis botrys, increased in response to the combination of elevated temperature and increased water colour. Furthermore, population fluctuations in M. botrys explained the majority of the variations in microcystin concentrations, suggesting that this species was responsible for the more than 300% higher microcystin concentrations in the future scenario treatment compared to the ambient scenario. Hence, it was not a change in cyanobacterial biomass, but rather a species‐specific response that had the most profound impact on bloom toxicity. We argue that understanding such species‐specific responses to multiple stressors is crucial for proper management decisions because toxic blooms can significantly affect both biodiversity and ecosystem functioning, as well as ecosystem services such as drinking water supply and recreation.

Globally, freshwater ecosystems are warming at unprecedented rates and northern temperate lakes are simultaneously experiencing increased runoff of humic substances (brownification), with little known consequences for future conservation of biodiversity and ecosystem functioning. We employed an outdoor mesocosm experiment during spring and summer to investigate the combined effects of gradually increasing warming and brownification perturbations on the phytoplankton community structure (biodiversity and composition) and functioning (biomass). While we did not observe overall significant treatment effects on total phytoplankton biomasses, we show that predicted increases in warming and brownification can reduce biodiversity considerably, occasionally up to 90% of Shannon diversity estimates. Our results demonstrate that the loss of biodiversity is driven by the dominance of mixotrophic algae (Dinobryon and Cryptomonas), whereas several other phytoplankton taxa may be temporarily displaced from the community, including Cyclotella, Desmodesmus, Monoraphidium, Tetraedron, Nitzschia and Golenkinia. The observed loss of biodiversity coincided with an increase in bacterial production providing resources for potential mixotrophs along the gradient of warming and brownification. This coupling between bacterial production and mixotrophs was likely a major cause behind the competitive displacement of obligate phototrophs and supports evidence for the importance of consumer–prey dynamics in shaping environmental impacts on phytoplankton communities. We conclude that warming and brownification are likely to cause a profound loss of biodiversity by indirectly affecting competitive interactions among phytoplankton taxa. Importantly, our results did not show an abrupt loss of biodiversity; instead the reduction in taxa richness levelled off after exceeding a threshold of warming and brownification. These results exemplify the complex nonlinear responses of biodiversity to environmental perturbations and provide further insights for predicting biodiversity patterns to the future warming and brownification of freshwaters.