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 management 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 originated 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 original 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 journals; providing in fine a better understanding of lakes’ ecosystems functioning under local and global pressures.

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.

As the global climate warms, the fate of lacustrine fish is of huge concern, especially given their sensitivity as ectotherms to changes in water temperature. The Arctic charr (Salvelinus alpinus L.) is a salmonid with a Holarctic distribution, with peripheral populations persisting at temperate latitudes, where it is found only in sufficiently cold, deep lakes. Thus, warmer temperatures in these habitats particularly during early life stages could have catastrophic consequences on population dynamics. Here, we combined lake temperature observations, a 1-D hydrodynamic model, and a multi-decadal climate reanalysis to show coherence in warming winter water temperatures in four European charr lakes near the southernmost limit of the species’ distribution. Current maximum and mean winter temperatures are on average ~ 1 °C warmer compared to early the 1980s, and temperatures of 8.5 °C, adverse for high charr egg survival, have frequently been exceeded in recent winters. Simulations of winter lake temperatures toward century-end showed that these warming trends will continue, with further increases of 3–4 °C projected. An additional 324 total accumulated degree-days during winter is projected on average across lakes, which could impair egg quality and viability. We suggest that the perpetuating winter warming trends shown here will imperil the future status of these lakes as charr refugia and generally do not augur well for the fate of coldwater-adapted lake fish in a warming climate.

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.