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Climate warming is increasing thermal stratification depth, strength, and duration in lakes, leading to more frequent hypolimnetic oxygen depletion. Most research has focused on eutrophic temperate lakes, which differ significantly from boreal lakes that dominate Earth’s landscape. However, assessing the impact of hypoxia, confounded by browning, warming, and altered stratification, on biogeochemistry and ecological processes in boreal lakes is particularly challenging. Here, we test how oxygenating a hypoxic hypolimnion affects water chemistry, bacterial and primary production (BP and PP), and detritus degradation in a shallow humic boreal lake divided into two basins in an experimental four-year Before-After Control-Impact (BACI) design. After two control years, we oxygenated the hypolimnion of one basin during two stratified periods without disturbing the seasonal development of the thermocline. Hypolimnetic oxygen concentrations moderately impacted lake biogeochemistry. Reoxygenation altered nitrification pathways (increased NO3−) of the hypolimnion, and slightly decreased epilimnion and lake BP (− 6.1% of annual average) and green tea degradation (− 6.0%), whereas Rooibos degradation slightly increased (7.3%). Other water chemistry parameters remained within natural variation. We compared our BACI approach, which separates natural variation, to the simpler Before vs After approach, which does not. We find that studies not accounting for seasonal and among-year variability may overestimate the effects of oxygenation on hypolimnion biogeochemistry, as much of the observed impact is due to natural climate variation. Climate warming and altered stratification patterns are therefore likely to impact boreal lake algal and bacterial production and degradation more than hypolimnion hypoxia during the stratified period.

Climate change represents a serious threat to aquatic ecosystems, with an increase in lake temperatures already observed that is expected to continue in the near future. Aside from the direct effects of warming, climate change is also partially responsible for the browning of lakes. Browning is an ongoing phenomenon related to the increased export of terrestrial dissolved organic matter into lakes. With ongoing climate changes, lakes are becoming warmer and browner. This has major impacts on the food web dynamics of these systems. Many studies have previously examined the effects of warming and browning on consumer responses, mainly through spatial surveys. However, a mechanistic understanding of how consumers in the food web will respond to simultaneously occurring warming and browning remains poorly understood.  

Using two large-scale ecosystem experiments, I studied the effects of warming and browning on consumer growth, size-structure, and population responses, and the potential mechanisms that dictate the emergent responses. In general, warming led to reduced consumer biomass and size structure, whilst browning led to an increase. Specifically, warming reduced intermediate consumer biomass and fish top consumer abundance, biomass and size structure, while browning either led to little to no changes in intermediate consumers, but increased fish top consumer abundance, biomass, and production. However, these responses were determined by food-web structure, interactions, and context-dependent mechanisms. This thesis advances our understanding of the mechanisms that drive changes in consumer responses to warming and browning and provides a better understanding of how ongoing climate may affect the structure and functioning of freshwater ecosystems.  

1. Globally, lakes are warming and browning with ongoing climate change. These changes significantly impact a lake's biogeochemical properties and all organisms, including invertebrate consumers. The effects of these changes are essential to understand, especially during critical periods after and before the growing season, that is, autumn and spring, which can determine the composition of the invertebrate consumer community.
2. In this study, we used a large-scale experimental pond system to test the combined effect of warming (+3°C) and increased input of terrestrial and coloured dissolved organic carbon (gradient of 1.6–8.8 mg/L in the ambient and 1.6–9.3 mg/L in the warm)—which causes browning—on zooplankton and benthic macroinvertebrate biomass and composition during the autumn and the following spring.
3. Total zooplankton biomass decreased with warming and increased with browning, while total zoobenthos did not respond to either treatment. Warming and browning throughout the autumn had no overall interactive effects on zooplankton or zoobenthos. Autumnal warming decreased total pelagic consumer biomass, caused by a decrease in both Rotifera and Copepoda. In contrast, there was no effect on overall benthic consumer biomass, with only Asellus sp. biomass showing a negative response to warming. An autumnal increase in dissolved organic carbon led to increased total pelagic consumer biomass, which was related to increases in Daphnia sp. biomass but did not affect zoobenthos biomass. While we expected zooplankton and zoobenthos biomass to follow responses in primary and bacterial production to treatments, we did not find any relationship between consumer groups and these estimates of resource production.
4. Our results suggest that consumer responses to warming and browning during autumn may lead to less overarching general changes in consumer biomass, and responses are mostly taxon-specific.
5. This study gives novel insights into the effects of warming and browning on consumer biomass during autumn and spring and increases the understanding of the effects of climate change on invertebrate community biomass in the different habitats.

Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.