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.

Negative relationships between dissolved organic carbon (DOC) concentration and fish productivity have been reported from correlative studies across lakes, but to date there have not been experimental tests of these relationships. We increased the DOC concentration in a lake by 3.4 mg·L−1, using a before–after control–impact design, to quantify the effects on the productivity and population structure of largemouth bass (Micropterus salmoides). Greater DOC reduced the volume of the epilimnion, the preferred habitat of largemouth bass, resulting in increased bass density. The likelihood that adult bass had empty diets decreased despite this increase in bass density; diet composition also changed. There was no apparent change in bass growth or condition. Overall, there was no net change in largemouth bass productivity. However, changes in young of year and juvenile recruitment and feeding success suggest the possibility that future effects could occur. Our results are the first to examine the effects of an increase in DOC on fish productivity through a 5-year temporal lens, which demonstrates that the relationship between DOC and fish productivity is multidimensional and complex.

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.