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Acoustic cameras are increasingly used in monitoring studies of diadromous fish populations, even though analyzing them is time-consuming. In complex in situ contexts, anguilliform fish may be especially difficult to identify automatically using acoustic camera data because the undulation of their body frequently results in fragmented targets. Our study aimed to develop a method based on a succession of computer vision techniques, in order to automatically detect, identify and count anguilliform fish using data from multiple models of acoustic cameras. Indeed, several models of cameras, owning specific technical characteristics, are used to monitor fish populations, causing major differences in the recorded data shapes and resolutions. The method was applied to two large datasets recorded at two distinct monitoring sites with populations of European eels with different length distributions. The method yielded promising results for large eels, with more than 75% of eels automatically identified successfully using datasets from ARIS and BlueView cameras. However, only 42% of eels shorter than 60 cm were detected, with the best model performances observed for detection ranges of 4–9 m. Although improvements are required to compensate for fish-length limitations, our cross-camera method is promising for automatically detecting and counting large eels in long-term monitoring studies in complex environments.

Lakes are essential ecosystems that provide a large number of ecosystem services whose quality is strongly impacted by human pressures. Optimal uses of lakes require adapted magement practices which in turn rely on physico-chemical and biological monitoring. Long-term ecological monitoring provides large sets of environmental data. When such data are available, they have to be associated to metadata and to be stored properly to be accessible and useable by the scientific community. We present a data informatics system accessible to anyone who requests it. Maintained online since 2014 (https://si-ola.inrae.fr), it is origited from the Observatory on LAkes (OLA). It contains long-term data from 4 peri-alpine lakes (Lakes Aiguebelette, Annecy, Bourget, Geneva/Léman) and 24 high-altitude lakes of the northern French Alps. We describe the generated long-term data series, the data type, the methodologies and quality control procedures, and the information system where data are made accessible. Data use is allowed under the condition of providing reference to the origil source. We show here how such a platform clearly enhances data sharing and scientific collaboration. Various studies referring to these data are regularly published in peer-reviewed jourls; providing in fine a better understanding of lakes’ ecosystems functioning under local and global pressures.

Alterations in the acoustic environment owing to anthropogenic sound are recognised as global pollution and strengthening studies in freshwater. This study focuses on the impact of lake seismic surveys on fish. First, we measured individual stress responses, i.e. cortisol levels and oxidative stress, morphological parameters, and stomach contents of juvenile roaches (Rutilus rutilus) captured by trawling prior to and during the seismic survey. Second, using hydroacoustics, we analysed individual fish and school behaviour before, during, and after the shots. We collected environmental DNA (eDNA) and analysed the concentrations of three species to assess their littoral refuge. Finally, using hydroacoustics, we assessed pelagic fish density before, during, and after the shots. We demonstrated that the shots noticeably impacted juvenile roaches, from the molecular and cellular level to individual morphological characteristics. During the seismic shots, changes in school characteristics were observed. At the onset of the seismic survey, a sharp decrease (> 30%) in pelagic fish density was observed, and no increase in fish density in the littoral area was noted for the three species. These responses suggest that sound disturbances due to air gun shots affect fish in multiple ways (physiology, morphology, behaviour, and habitat use) and across multiple biological scales.

A dramatic slowing down of acoustic wave transport in dense fish shoals is observed in open-sea fish cages. By employing a multi-beam ultrasonic antenna, we observe the coherent backscattering phenomenon. We extract key parameters of wave transport such as the transport mean free path and the energy transport velocity of diffusive waves from diffusion theory fits to the experimental data. The energy transport velocity is found to be about 10 times smaller than the speed of sound in water, a value that is exceptionally low compared with most observations in acoustics. By studying different models of the fish body, we explain the basic mechanism responsible for the observed very slow transport of ultrasonic waves in dense fish shoals. Our results show that, while the fish swim bladder plays an important role in wave scattering, other organs have to be considered to explain ultra-low energy transport velocities.

Synchronic variations in abundance in populations of the same species are common phenomena encountered in various environments, including lakes, and different taxa of freshwater fishes. This phenomenon can be caused by similar environmental conditions across physically separated populations. In the context of the ongoing climate change, it is essential to test this hypothesis, identify the factors driving the synchrony and elucidate the mechanisms, in the attempt to improve fisheries management. This study investigates synchronic variations in European whitefish (Coregonus spp.) populations in five peri-alpine lakes. The hypothesis suggests that shared biotic or abiotic factors contribute to similar trends in whitefish landings. Environmental and seasonal variables impacting the early life stages of the species were analyzed, and the Euclidean distances between the multivariate time series were calculated to identify similarities or dissimilarities in lake environmental parameters. We found that regional winter and spring temperatures were consistent across the lakes, but these factors did not fully account for variations in landings statistics. Wind intensity, water level and zooplankton abundance showed lake-specific patterns that could better explain local conditions and dynamics. Linear models did not reveal a coherent correlation with a common environmental variable across all lakes. However, distinct relationships were found in four of the lakes, with local factors significantly contributing to abundance variations. The spring abundance of Daphnia spp., a primary food source for whitefish larvae, was the main factor correlated with fish landing trends in Lake Geneva and Lake Bourget. Higher availability of Daphnia spp. may decrease intraspecific competition and density-dependent mortality. In Lake Neuchâtel, winter water temperature was negatively correlated with fish abundance proxies, suggesting that warmer winters may compromise reproduction success. Lake Annecy saw an increase in whitefish landings following a substantial reduction in fishing efforts during the late 2000s. A significant negative correlation was found between whitefish landings and fishing efforts. No relationship was found for Lake Aiguebelette, maybe due to a lack of zooplankton data. In conclusion, the observed synchrony in the European whitefish population is likely driven by a combination of interacting environmental and anthropogenic factors rather than a single common variable. Further research and a more detailed dataset are needed to better understand these complex relationships.   Cover image: Whitefish (courtesy of Rémi Masson)

The thermal dependence of metabolism has attracted much attention because metabolism is linked to many ecological properties, from individuals to ecosystems. The rate at which physiological traits change is an important factor to account for when assessing thermal plasticity since the time of exposure might allow organisms to compensate for the effect of temperature on performance. Here, we studied short‐ and long‐term thermal plasticity of metabolic rate and its scaling with body mass of Alpine charr (Salvelinus umbla). To do so, we raised juveniles from Lake Geneva at 4.5°C and 8.5°C, measured their routine metabolic rate at their incubation temperature (long exposure, > 6 months), and individuals raised at 4.5°C were also tested at 8.5°C (short exposure, < 24 h). The metabolic rate of Alpine charr increased with temperature, as theoretically expected. We found no effects of duration of exposure on metabolic rate or its scaling with body mass. Despite a long‐term exposure to higher temperature, individuals did not adjust their metabolic rate as compared to individuals exposed to a rapid increase in temperature, questioning the capacity of Alpine charr to compensate for temperature increase through their metabolic rate. Therefore, our data reveal no compensation mechanisms of Alpine charr to counterbalance the acute effect of temperature. Further studies will be required to fully understand the adaptive potential of Alpine charr in the context of global change. The rate at which phenotypic plasticity occurs is now acknowledged to be an important factor to account for when studying plasticity, as it allows to understand how organisms can respond to rapid environmental changes. Using Alpine charr (Salvelinus umbla) as a model species, we found that time of exposure to higher temperature did not alter metabolic rate or its scaling with body mass. Interestingly, Alpine charrs are considered stenothermic species, and our results suggest that their adaptive capacities and their potential evolution in warmer and less predictable environments might be questioned.

Hydroacoustics has become a requisite method to assess fish populations and allows to describe the relationships of fish with other elements of the aquatic ecosystem. This nonintrusive method is currently an integral part of the sampling procedures recommended for fish stock assessment by the Water Framework Directive and has been standardized by the European Committee for Standardization [CEN (2014) CSN EN 15910 ‐ Water quality ‐ Guidance on the estimation of fish abundance with mobile hydroacoustic methods, Category: 7577 Water quality. Biological.]. In Europe, hydroacoustic surveys are performed in freshwater using different frequencies. Consequently, there is a need to evaluate if survey results can be compared. This study aimed to carry out in situ comparisons at the 38 kHz frequency (noted f) with two other commonly used frequencies, 70 and 200 kHz. The 38 kHz frequency has seldom been compared with other frequencies in freshwater although it is widely used worldwide, especially in the Great Lakes of North America and in Sweden. In 2016, hydroacoustic data were acquired in Lakes Annecy and Bourget using methods validated in previous studies that compared the frequencies 70, 120 and 200 kHz. This study showed similar density and biomass estimations as a function of frequency, density(f) and biomass(f), between the frequencies studied for low to moderate fish densities. For higher fish densities, the results were more variable and need to be verified. Fish density(f) and biomass(f) estimations sometimes exhibit differences between frequencies, which is not fully in agreement with theoretical calculations. The aim of this study was to evaluate frequency comparisons in practise. However, if the differences on acoustic metrics, density(f) or biomass(f) between frequencies were occasionally statistically significant, the differences were small enough to be considered negligible for fish population management. These analyses led to better knowledge of the responses from fish in temperate lakes for the studied frequencies. Our findings should be considered when revising the CEN standard. Hydroacoustics has become a requisite method to assess fish populations and allows to describe the relationships of fish with other elements of the aquatic ecosystem. In Europe, hydroacoustic surveys are performed in freshwater using different frequencies. Consequently, there is a need to evaluate if survey results can be compared. This study aimed to carry out in situ comparisons at the 38 kHz frequency with two other commonly used frequencies, 70 and 200 kHz. This study showed similar density(f) and biomass(f) estimations between the frequencies studied for low to moderate fish densities. For higher fish densities, the results were more variable and need to be verified.

Trophic interactions are central in understanding ecosystem processes and the management of natural ecosystems but are frequently complex to estimate. To address this issue, body size has been shown to be a useful trait to reconstruct species interactions, particularly in aquatic ecosystems. An allometric niche model (aNM) considering body size as a niche trait is proposed to predict trophic interactions in temperate freshwater ecosystems. The aNM calibration was based on 26 ubiquitous freshwater species with known minimal and maximum prey body sizes that permitted the establishment of prey body size ranges for vertebrate and invertebrate consumers. The aNM inferences were validated for 13 empirical freshwater food webs, and the model was applied to an extensive inventory of 474 species (spanning six orders of body size magnitude) from the largest natural French lake (Lake Bourget). This application permitted to strengthen the aNM validation with predator‐prey mass ratio comparisons, predicted diet analyses, and allowed the exploration of the lake food web structure. The aNM provided appreciable intrinsic validity (specificity = 87 ± 12%, sensitivity = 59 ± 29%, accuracy = 81 ± 10%), and departures among inferred and empirical trophic interactions were explained by foraging specificities or limited sampling of stomach contents. In Lake Bourget, 26,037 trophic links were inferred. Predator–prey mass ratios for vertebrates and invertebrates were consistent with those empirically established and were occasionally higher for invertebrates as the aNM considers small prey (e.g., bacteria) as possible resources for invertebrates. The inferred diets for three species selected for their well‐known foraging ecology also revealed plausible outcomes of the aNM. The nested structure of the lake food web was determined by highlighting different topologies among the benthic and the pelagic food sub‐webs and the role of top predator fish in the coupling of both food sub‐webs. Due to the large number of species inventories available worldwide for freshwater ecosystems anchored in the ecological monitoring, the aNM may represent a valuable tool for both ecologists and managers to address complementary facets of applied biodiversity studies (e.g., reconstruct highly resolved food webs, predict pressures on important species or new interactions with invasive species).

Through cascading effects within lake food webs, commercial and recreational fisheries may indirectly affect the abundances of organisms at lower trophic levels, such as phytoplankton, even if they are not directly consumed. So far, interactive effects of fisheries, changing trophic state and climate upon lake ecosystems have been largely overlooked. Here we analyse case studies from five European lake basins of differing trophic states (Lake Võrtsjärv, two basins of Windermere, Lake Geneva and Lake Maggiore) with long-term limnological and fisheries data. Decreasing phosphorus concentrations (re-oligotrophication) and increasing water temperatures have been reported in all five lake basins, while phytoplankton concentration has decreased only slightly or even increased in some cases. To examine possible ecosystem-scale effects of fisheries, we analysed correlations between fish and fisheries data, and other food web components and environmental factors. Re-oligotrophication over different ranges of the trophic scale induced different fish responsesIn the deeper lakes Geneva and Maggiore, we found a stronger link between phytoplankton and planktivorous fish and thus a more important cascading top-down effect than in other lakes. This connection makes careful ecosystem-based fisheries management extremely important for maintaining high water quality in such systems. We also demonstrated that increasing water temperature might favour piscivores at low phosphorus loading, but suppresses them at high phosphorus loading and might thus either enhance or diminish the cascading top-down control over phytoplankton with strong implications for water quality.

Acoustic cameras are increasingly used in monitoring studies of diadromous fish populations, even though analyzing them is time-consuming. In complex in situ contexts, anguilliform fish may be especially difficult to identify automatically using acoustic camera data because the undulation of their body frequently results in fragmented targets. Our study aimed to develop a method based on a succession of computer vision techniques, in order to automatically detect, identify and count anguilliform fish using data from multiple models of acoustic cameras. Indeed, several models of cameras, owning specific technical characteristics, are used to monitor fish populations, causing major differences in the recorded data shapes and resolutions. The method was applied to two large datasets recorded at two distinct monitoring sites with populations of European eels with different length distributions. The method yielded promising results for large eels, with more than 75% of eels automatically identified successfully using datasets from ARIS and BlueView cameras. However, only 42% of eels shorter than 60 cm were detected, with the best model performances observed for detection ranges of 4–9 m. Although improvements are required to compensate for fish-length limitations, our cross-camera method is promising for automatically detecting and counting large eels in long-term monitoring studies in complex environments.