Isotope turnover in muscle of ectotherms depends primarily on growth rather than on metabolic replacement. Ectotherms, such as fish, have a discontinuous pattern of growth over the year, so the isotopic signature of muscle (delta13C and delta15N) may only reflect food consumed during periods of growth. In contrast, the liver is a regulatory tissue, with a continuous protein turnover. Therefore, the isotopic composition of liver should respond year round to changes in the isotopic signature of food sources. Therefore, we predicted that (1) Whitefish in Lake Geneva would have larger seasonal variation in the isotopic variation of the liver compared to that of the muscle tissue, and (2) the isotope composition of fish muscle would reflect a long-term image of the isotope composition of the food consumed only throughout the growth period. To test these expectations, we compared the isotope compositions of Whitefish muscle, liver and food in a 20-month study. We found that the seasonal amplitude of isotope variation was two to three times higher in liver compared to muscle tissue. During the autumn and winter, when growth was limited, only the isotopic signature of liver responded to changes in the isotope composition of the food sources. The delta13C and delta15N of muscle tissue only reflected the food consumed during the spring and summer growth period.

The spread of hypoxia is a threat to aquatic ecosystem functions and services as well as to biodiversity. However, sparse long-term monitoring of lake ecosystems has prevented reconstruction of global hypoxia dynamics while inhibiting investigations into its causes and assessing the resilience capacity of these systems. This study compiles the onset and duration of hypoxia recorded in sediments of 365 lakes worldwide since AD 1700, showing that lacustrine hypoxia started spreading before AD 1900, 70 years prior to hypoxia in coastal zones. This study also shows that the increase of human activities and nutrient release is leading to hypoxia onset. No correlations were found with changes in precipitation or temperature. There is no evidence for a post-1980s return to well-oxygenated lacustrine conditions in industrialized countries despite the implementation of restoration programs. The apparent establishment of stable hypoxic conditions prior to AD 1900 highlights the challenges of a growing nutrient demand, accompanied by increasing global nutrient emissions of our industrialized societies, and climate change.

The scales of whitefish Coregonus lavaretus were used in place of dorsal muscle, which necessitates killing the fish, to study food webs from the δ13C and δ15N isotopic ratios in the organic fraction. As scales are composed of both organic and calcified fractions, a protocol for scale decalcification was first devised. The δ13C and δ15N values of the decalcified scales were then shown to be closely correlated to those of the dorsal muscle, demonstrating that scales could be used in place of muscle to study food webs. Changes in the δ13C of whitefish were determined from a scale collection that extended over the period during which the trophic state of Lake Geneva was recovering.

Summary1. Fatty acid-specific stable isotope analysis (FA-SIA) is expected to encompass most of the limits encountered when using more classical trophic markers such as bulk tissue stable isotope or fatty acid analyses. However, an essential premise for using FA-SIA for trophic studies is that the individual FA d 13C values of the consumer reflect those of its diet. Field studies using FA-SIA have so far made this assumption, which is not necessarily supported by the rare experimental tests. 2. A feeding experiment was conducted on Daphnia to test whether the d 13C values of individual fatty acids in Daphnia were actually related to those of its food. 3. Only the stable isotope composition of polyunsaturated (PUFA) and branched fatty acids (BrFA) was globally transmitted from the diet to Daphnia lipids, with however a significant isotope fractionation that varied depending on the considered diet source. 4. A model was constructed to evaluate how such variability may affect the reliability of FA-SIA to track the dietary sources of consumers' PUFA and BrFA in the field. Results suggest that provided the endmembers are substantially isotopically different, FA-SIA could provide valuable insights into the pathways conveying these particular FA to consumers in the field.

High-throughput sequencing of sedimentary DNA (sed-DNA) was utilized to reconstruct the temporal dynamics of microbial eukaryotic communities (MECs) at a centennial scale in two re-oligotrophicated lakes that were exposed to different levels of phosphorus enrichment. The temporal changes within the MECs were expressed in terms of richness, composition and community structure to investigate their relationships with two key forcing factors (i.e., nutrient enrichment and climate warming). Various groups, including Apicomplexa, Cercozoa, Chrysophyceae, Ciliophora, Chlorophyceae and Dinophyceae, responded to phosphorus enrichment levels with either positive or negative impacts on their richness and relative abundance. For both lakes, statistical modelling demonstrated that phosphorus concentration ([P]) was a dominant contributor to MECs modifications before the 1980s; after the mid-80s, the contribution of air temperature changes increased and potentially surpassed the contribution of [P]. Co-occurrence network analysis revealed that some clusters of taxa (i.e., modules) composed mainly of Dinophyceae and unclassified Alveolata were strongly correlated to air temperature in both lakes. Overall, our data showed that sed-DNA constitutes a precious archive of information on past biodiversity changes, allowing the study of the dynamics of numerous eukaryotic groups that were not traditionally considered in paleo-reconstructions.