Salmonids are introduced in various ecosystems, including mountain lakes characterised by extreme environmental constraints. Although these constraints can affect salmonid body condition through direct and indirect pathways, they remain seldom explored despite their importance for understanding salmonid fitness and long-term establishment.In order to fill this gap, we firstly fitted species-specific weight-length relationships for three salmonid species in nine mountain lakes, and compared their allometric coefficients with those of 362 salmonid populations worldwide to identify potential differences in growth trajectory of salmonids in the studied lakes. We then investigated how thermal characteristics and lake morphometry could influence salmonid body conditions, both directly and indirectly through salmonid density, the presence of forage fish and resource densities. We calculated salmonid relative body condition Kn and used a structural equation model (SEM) to disentangle these direct and indirect effects.The values of allometric coefficients for the three species did not differ from those of most salmonids worldwide although ontogenetic changes in Salvelinus alpinus weight gain was observed. Kn differed significantly among the populations studied. The strongest effects were related to direct and indirect effects of lake morphometry, while thermal characteristics had mostly indirect effects on Kn. The strength and the sign of the indirect effects of morphometry and temperature were mediated by the direct effects of resource and salmonid densities on Kn.Kn estimates were greater in lakes with shallow basin slopes than those with steep slopes. Shallow basin slopes probably provide habitats that support high prey availability and require lower energy expenditure by salmonids compared to lakes with steep slopes dominated by pelagic habitats. Complementarily, higher winter and summer temperatures favour Kn by supporting higher prey densities and longer periods of feeding activity. Our results may help managers to select lakes that optimise sustainability of salmonid populations based on the joint effects of basin morphometry and the expected thermal modifications induced by global change.

Lakes host a high level of biodiversity, especially in their littoral zone, and provide various ecological and socio-economic services. Lake ecosystems are impacted by a combination of pressures from different human activities (industry, hydroelectricity, agriculture, recreational activities, domestic and urban uses). Anthropic pressures can lead to alterations and dysfunctions in lakes, particularly in the littoral zone. The 2000 EU Water Framework Directive led to considerable efforts to improve the ecological status of European water bodies. However, in France, measures implemented by lake managers to counteract, limit or suppress anthropogenic impacts are still poorly identified. Moreover, their effects on hydromorphology, physico-chemistry and biotic communities are often only partially reported (the monitoring being incomplete or heterogeneous, if not missing). This paper proposes a framework to harmonize the monitoring of habitat improvement actions conducted in the littoral zone of lakes. The monitoring method is presented as well as the sampling protocols and techniques set out to survey both the restored and control zones at the European French territory scale. Long-term monitoring of hydromorphological, biological and physicochemical features is expected to improve our understanding of recolonization mechanisms following restoration. The proposed approach will therefore guide practitioners to identify the best restoration options and ultimately contribute to the conservation of recipient populations and communities.

Species introductions can alter local food-web structure by changing the vertical or horizontal diversity within communities, largely driven by their body size distributions. Increasing vertical and horizontal diversities is predicted to have opposing effects on stability. However, their interactive effects remain largely overlooked. We investigated the independent and collective effects of vertical and horizontal diversities on food-web stability in alpine lakes stocked with variable body size distributions of introduced fish species. Introduced predators destabilize food-webs by increasing vertical diversity through food chain lengthening. Alternatively, increasing horizontal diversity results in more stable food-web topologies. A non-linear interaction between vertical and horizontal diversities suggests that increasing vertical diversity is most destabilizing when horizontal diversity is low. Our findings suggest that the size structure of introduced predators drives their impacts on stability by modifying the structure of food-webs, and highlights the interactive effects of vertical and horizontal diversities on stability.

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

The management of lakes requires the definition of physico-chemical thresholds to be used for ecosystem preservation or restoration. According to the European Water Framework Directive, the limits between physico-chemical quality classesmust be set consistently with biological quality elements. Onewayto do this consists in analyzing the response of aquatic communities to environmental gradients across monitoring sites and in identifying ecological community thresholds, i.e. zones in the gradients where the species turnover is the highest. In this study, fish data from196 lakes in France were considered to derive ecological thresholds using the multivariate method of gradient forest. The analysis was performed on 25 species and 36 environmental parameters. The results revealed the highest importance of maximal water temperature in the distribution of fish species. Other important parameters includedgeographical factors, dissolved organic carbon concentration and water transparency, while nutrients appeared to have low influence. In spite of the diversity of species responses to the gradients, community thresholds were detected in the gradients of the most important physico- chemical parameters and of total phosphorus and nitrate concentrations as well. The thresholds identified in such macroecological study may highlight new patterns of species natural distribution and improve niche characterization. Moreover, when factors that may be influenced by human activities are involved, the thresholds could be used to set environmental standards for lake preservation.

In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.

Ecological research and monitoring of lacustrine ecosystems often requires a whole-lake assessment of fish communities. Gillnet sampling offers an efficient means of estimating abundance, biomass and fish community composition. However the choice of gillnet sampling protocol may influence lake characterization via physical properties of the nets and allocation of sampling effort between littoral, benthic and pelagic habitats. This paper compares two commonly used, whole-lake sampling protocols applied across 17 prealpine, subalpine and alpine European lakes ranging widely in size, depth and altitude to determine their relative strength for research and management applications. Effort-corrected estimates of abundance, biomass and species richness were correlated between the protocols and both distinguished the trout-dominated alpine communities from subalpine and prealpine lakes dominated by whitefish and perch. A considerable amount of variance remained unexplained between the two protocols however, which seemed to correspond with differences in the proportion of effort among benthic and pelagic habitats. We suggest that both the European standard (CEN) and vertical (VERT) netting protocols are suitable for assessing ecological status and monitoring changes in lake fish communities through time. However the details of each protocol should be kept in mind when comparing fish communities between lakes. Mesh sizes used in CEN nets produce a more even size frequency distribution, suggesting that this protocol is most appropriate for assessing size structure of fish assemblages. The high proportion of netting effort in benthic habitats shallower than 70m depth under the CEN protocol means that, particularly in larger lakes, outcomes will be disproportionately influenced by the ecological condition of this habitat. The VERT protocol presumably provides a more accurate estimate of whole-lake CPUE and community composition because effort, in terms of net area, is more evenly distributed across the entire volume of the lake. This is particularly important in large and deep lakes where pelagic habitats occupy a high proportion of the lake volume.