La définition d’états de référence joue un rôle clé en restauration écologique, en servant de point de repère pour évaluer la dynamique de restauration des écosystèmes. Toutefois, le choix de cette référence n'est jamais totalement objectif et dépend de nombreux facteurs contextuels, tels que l’histoire et la géographie du site, son intégrité écologique initiale, ou les intérêts des parties prenantes. Pour éclairer les choix effectués lors de la définition des états de référence en restauration écologique, nous avons analysé 32 projets de restauration mis en œuvre et suivis dans une diversité d’écosystèmes terrestres et aquatiques entre 1999 et 2023 par des chercheurs du réseau « Restauration écologique INRAE » (REI, https://restauration-ecologique.hub.inrae.fr). Nos résultats mettent en évidence des tendances commune dans les critères mobilisés pour la sélection des références, tout en révélant des degrés d’accord variable entre projets, avec des différences notables entre les projets aquatiques et terrestres en termes d'implication des parties prenantes, des métriques choisies et des mesures d'évaluation. Cette étude constitue une première étape avant une enquête au sein de la communauté scientifique internationale. L’objectif est ainsi d’explorer plus en profondeur les défis liés à la définition des états de référence, en particulier dans le contexte d’accélération des changements globaux (notamment climatiques) et celui de la mise en œuvre du nouveau règlement sur la restauration de la nature dans les États membres de l’Union européenne.

Les conditions hydrologiques et morphologiques des lacs contribuent à structurer les habitats pour la faune et la flore et constituent à ce titre un élément clé du bon fonctionnement de ces écosystèmes. De ce fait, une meilleure prise en compte dans les politiques de gestion de l'eau et des milieux est indispensable, ce qu'impose la directive cadre européenne sur l'eau depuis le début des années 2000. Pour pallier les lacunes opérationnelles et permettre à la France de répondre à ses obligations réglementaires, le Pôle R&D ECLA (Pôle Recherche et Développement Écosystèmes Lacustres) a développé plusieurs méthodes complémentaires de description et de suivi des caractéristiques hydromorphologiques des lacs. Les informations recueillies, combinées à des données auxiliaires issues de sources nationales, ont contribué au développement de l'indicateur LHYMO permettant de rendre compte du degré d'altération de ces caractéristiques au travers de quinze métriques. L'application de cet indicateur a permis pour la première fois de donner une vision nationale uniformisée de l'altération hydromorphologique des lacs français et ce quelle que soit leur origine (naturelle ou humaine). Les analyses les plus récentes concernant l'impact de ces altérations sur la faune et la flore lacustres montrent par ailleurs que les métriques issues de l'indicateur LHYMO sont en mesure d'expliquer une partie de la variabilité d'abondance taxonomique des compartiments biologiques étudiés, avec un degré d'influence variable selon les compartiments. Des résultats encourageants en vue d'une meilleure prise en compte des réponses biologiques et des enjeux de biodiversité sur les lacs.

The body size spectrum (or individual size distribution) is a simple yet widely recognized approach that links individual and population traits to community structure and ecosystem functions, making it a valuable indicator of anthropogenic effects. However, the assessment of size spectra in the context of biological invasions remains poorly explored. We investigated the impacts of non-native (NN) fish invasions on the size structure of 667 lacustrine fish communities across climatic regions (temperate, tropical, and subtropical systems) and the roles of trophic position and temperature in modulating these effects. We found that fish communities under higher invasion pressure exhibit flatter, or less negative, size spectrum exponents. Also, NN species from lower trophic levels can have greater impacts than piscivorous NNs by reshaping size spectra and reducing the overall biomass of native communities. We also observed that piscivore NNs and NNs from lower trophic levels interacted positively with temperature to drive the size spectrum exponent and total biomass of the native communities, respectively. These results can be explained by two main mechanisms: (i) NN piscivores primarily act through size-selective predation (top-down control), which may be intensified particularly on small prey in warmer lakes, and (ii) NN fish from lower trophic levels primarily act through competition, hence reducing the numerical abundance of small-sized native fish, which may be more vulnerable in colder and less productive lakes. These mechanisms are leading to flatter size spectrum exponents mainly at higher temperatures and to a decline in the total biomass of the native community, mainly at lower temperatures, effectively reversing the expected temperature-size rule pattern. By disentangling the trophic and temperature-dependent mechanisms through which NN fishes affect size structure, this study strengthens our ability to anticipate the impact of biological invasions on freshwater communities and their ecosystem functions and services under global change.

Pendant plus de dix ans, plusieurs travaux ont été menés au Pôle R&D ECLA (Pôle Recherche et Développement Écosystèmes Lacustres) pour développer les indices utilisant l’ichtyofaune permettant d’évaluer l’état écologique des lacs naturels et du potentiel écologique des retenues françaises. Ces indices reposent sur des relations statistiques établies entre les facteurs de stress et certaines caractéristiques taxonomiques ou fonctionnelles des communautés. Les indices développés, IIL pour les lacs naturels et IIR pour les retenues, rendent compte du niveau d’eutrophisation des plans d’eau. L’IIR répond également aux introductions d’espèces non natives. Au-delà du développement de ces indices, quelques sources d’incertitudes associées à l’évaluation de l’état écologique des plans d’eau ont été explorées. Nous avons montré que les incertitudes associées aux modèles permettent d’estimer la probabilité d’appartenance d’un lac à chaque classe d’état mais que la date d’échantillonnage et les interactions de pressions pouvaient influencer le classement des plans d’eau dans ces différentes classes d’état. Ces recherches ont trouvé un prolongement dans le développement d’un indice de vulnérabilité au risque de perte de biodiversité. Outre l’amélioration potentielle de ces indices, de nouveaux indicateurs sont attendus notamment dans le contexte de la restauration et le travail devra se poursuivre en intégrant les acquis de ces dix années de recherche.

Pour répondre à la nécessité prégnante de mettre en œuvre des mesures de restauration écologique efficaces sur les milieux, intimée notamment par le nouveau Règlement restauration de la nature, le pôle R&D ECLA (Pôle Recherche et Développement Écosystèmes Lacustres), a initié le projet des sites de démonstration en plans d’eau en 2016. Il s’agit de mettre en œuvre, sur un réseau de sites faisant l’objet d’un projet de restauration de zones littorales lacustres, un suivi standardisé et à long-terme des habitats et des communautés avant et après la réalisation des travaux. À travers des études multisites sur l’ensemble du territoire national, ce projet vise à améliorer significativement les connaissances en écologie de la restauration et à optimiser les pratiques, en identifiant les plus efficaces. Aujourd’hui constitué de treize sites issus de contextes variés et sur lesquels les travaux de restauration mis en œuvre sont d’ordre divers (reprofilage de berges, diversification d’habitats hors berge, restauration de roselières ou revégétalisation), le réseau des sites de démonstration en plans d’eau ambitionne d’intégrer l’ensemble des opérations portées par des partenaires prêts à rejoindre le réseau. Mettant l’accent sur le lien entre les parties prenantes du projet, il permet de nombreux échanges entre les sphères opérationnelle et scientifique, mais aussi entre les gestionnaires eux-mêmes.

Hydromorphological conditions are among the key determinants of the composition and abundance of biological assemblages in lakes. Consequently, hydromorphological alterations can significantly affect aquatic biodiversity and ecological status of lake ecosystems. Internationally, various methods have been developed to monitor and assess hydrological and morphological status, with particularly comprehensive efforts in Europe under the Water Framework Directive (WFD). In this study, we compiled and reviewed hydrological and morphological metrics included in 13 assessment methods currently used in Europe to assess lake hydromorphological conditions. These methods are applicable to both natural and man-made lakes and are designed to support the implementation of the WFD. We categorized the metrics by spatial scale, affected processes, and data requirements, to inform a more strategic selection of metrics and improve their alignment with lake management and restoration strategies. Of the metrics reviewed, those that refer to changes in water flows and littoral habitat quality are best described. In contrast, changes in the hydrological connection between the lake and groundwater are rarely assessed. Ongoing methodological advancements and emerging technologies, particularly in remote sensing, are expected to improve the accuracy and efficiency of hydromorphological alteration assessments in lakes. Future research needs are highlighted to address knowledge gaps regarding how climate change affects the hydrological and morphological characteristics of lakes, and, in particular to distinguish anthropogenic impacts on lake ecosystems from large-scale processes. A clearer understanding of these dynamics is essential for developing effective lake restoration strategies in the face of climate change.

According to differences in life history and species niches, community assembly processes are predicted to differ between common and rare species. While neutral processes, in particular dispersal, should contribute strongly to assembly of rare species, environmental filtering (species sorting) should dominate the community assembly of common species. We analysed commonness and rarity by occurrence, abundance and geographic range among 82 fish species in 1871 European lakes and reservoirs. The common 25% (21 species) were excluded, and structure and assembly processes of the 75% rare (61 species) species occurring in 348 lakes were evaluated. General linear latent variable models indicated that environmental variables related to lake type (lakes vs. reservoirs), climate and ecosystem size predicted a large proportion of variance for both rare species presence/absence and abundance models, while spatial variables (co-occurrence in watersheds) contributed little to the models. To link community structure with assembly processes, the contribution of seven fish traits related to life history, feeding and habitat preference to predicting the geographic range of the rare species was analysed by boosted regression trees. Intermediate average fecundity and high maximum body length of species predicted smaller geographic range and hence a higher level of rarity, but the response curves of the variables were mostly non-linear and difficult to interpret. In contrast to our assumption, the results of the dominant assembly processes and predictors for rare species were very similar to those predicted for the common fish species in lakes at the continental scale.

The continuous increase of anthropogenic activities reinforces their stress on aquatic ecosystems (from continental to marine ecosystems) that are the most altered ecosystems on Earth. To evaluate the risk of ecosystem decline toward human alterations, the concept of “ecological vulnerability” was developed to help managers to prioritize conservation actions. Various definitions of vulnerability and its components were used, but this concept is often centered on the intersection of three components: sensitivity, exposition, and adaptive capacity. The aim of this study was through a review of the scientific literature of the last 10 years, first to assess the goals of the use of the concept of vulnerability in aquatic ecology: for which pressure (e.g., climate change, predation) and organism, on which level of organization (individuals, species, …). The second objective, was to address the methods developed to assess vulnerability: which components were considered, which metrics were used, the scoring process… Fish were the organisms the most frequently concerned and the number of publications decreased with the increasing complexity of biodiversity studied (from populations to multitrophic organizations). Climate change was the main stressor for which vulnerability was assessed. Vulnerability was commonly defined as being highly sensitive, highly exposed and lowly adaptable even if adaptive capacity was rarely addressed. This study showed an interest in the concept of vulnerability to protect aquatic ecosystems. Nonetheless, to better evaluate their risk of biodiversity loss, we should consider vulnerability at a higher level of organization and encompass the adaptive capacity of the biota.

Hydromorphology provides a physical framework for aquatic biocenoses. Its condition directly affects the quality of habitats available for fauna and flora, and its assessment is therefore useful for biodiversity and water quality conservation, as well as for restoration programmes required by European and national directives.In this study, a site-specific index of Lake HYdroMOrphology, LHYMO, was developed to provide a quantitative assessment of the hydromorphological status of natural and non-natural lakes that is consistent with European Committee for Standardization (CEN) standards and that can be used for different purposes, including the implementation of the Water Framework Directive (WFD) and of the Habitats Directive.This new LHYMO index includes nine metrics related to the morphological WFD quality elements (QEs) and six metrics related to the hydrological WFD QEs, all of which are considered to support biological elements. The reference conditions were defined for each metric using an original approach: the degree of alteration is measured in relation to the natural characteristics of each lake, relative to a state that 'would be expected in the absence of disturbances'.Besides its use for regulatory purposes, this index is also a suitable tool for monitoring the efficacy of hydromorphological restoration projects or to help target effective conservation measures on lakes.Application of this index to 72 French lakes provides the first quantitative and homogeneous assessment of the hydromorphological quality of lakes over a whole territory and gives the first overview of the hydromorphological status of lakes in France, with classification into five classes ranging from 'high' to 'bad'.LHYMO is already operational for large French lakes as it relies mostly on reference datasets available at a national scale, and it may also be used in a wider scope through gathering or completing data from other sources.

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.

In view of the very strong degradation of aquatic ecosystems, it is urgent to set up monitoring systems that are best able to report on the effects of the stresses they undergo. This is particularly true in developing countries, where specific and relevant quality standards and funding for monitoring programs are lacking. The objective of this study was to make a relevant and objective choice of physicochemical parameters informative of the main stressors occurring on African lakes and to identify their alteration thresholds. Based on statistical analyses of the relationship between several driving forces and the physicochemical parameters of the Nokoué lagoon, relevant physicochemical parameters were selected for its monitoring. An innovative method based on Bayesian statistical modeling was used. Eleven physicochemical parameters were selected for their response to at least one stressor and their threshold quality standards also established: Total Phosphorus (<4.5mg/L), Orthophosphates (<0.2mg/L), Nitrates (<0.5 mg/L), TKN (<1.85 mg/L), Dry Organic Matter (<5 mg/L), Dissolved Oxygen (>4 mg/L), BOD (<11.6 mg/L), Salinity (7.6 ‰), Water Temperature (<28.7 °C), pH (>6.2), and Transparency (>0.9 m). According to the System for the Evaluation of Coastal Water Quality, these thresholds correspond to "good to medium" suitability classes, except for total phosphorus. One of the original features of this study is the use of the bounds of the credibility interval of the fixed-effect coefficients as local weathering standards for the characterization of the physicochemical status of this anthropized African ecosystem.

The main obstacles to monitoring aquatic ecosystems have always been the lack of data, the complex socio-economic context and the lack of specialised expertise that characterise the West African region. To overcome these challenges, it is necessary to invest in the definition of context-appropriate approaches that allow good ecological assessment, improve understanding of the functioning of these ecosystems and facilitate data collection. This study focused on using benthic macrofauna to assess the risks of moving away from Good Ecological Status towards the functioning of an anthropised system (Nokoué-Benin), based on the definition of reference values for macroinvertebrate metrics, stress thresholds and the responses of selected metrics to stressors. The approach used is a combination of a joint species distribution model and Bayesian networks. We used JSDM to select relevant metrics and generate posterior probabilities. We then converted these posterior probabilities into posterior response probabilities for each of the stress levels and fed them into a Bayesian network. We used the Bayesian network response predictions to define the reference values of the metrics and the stress thresholds derived from the probability density plots for the low pressure levels. An application of this approach was then carried out on a lagoon sampled during high and low water periods for three years, with 33 macroinvertebrate taxa present in all seasons and sampling points, and measurements of 14 environmental parameters used as application data. The relevance of the results, despite the small sample size, supports wider application of the approach in West Africa.

The characterization of lake hydromorphology is crucial to understand the dynamics of biodiversity. In Europe, it is also a regulatory requirement of the Water Framework Directive. However, according to the literature, few methods include this characterization. The aim of this study is to review the state of the art of the methods currently used or under development in European countries to assess lake hydromorphological status for the implementation of the WFD. Our analysis is based on responses to a questionnaire distributed to national experts on hydromorphology of the 28 countries implementing the WFD. Our results highlighted significant progress in the assessment of hydromorphological features and processes. Water level regime, through the range of water flow or existing water management, and structure of the shore zone through macrophytes and substrate characteristics or measurement of lateral connectivity, are the most frequently assessed features. Stratification, surface/groundwater connection and planform pattern are the lake features most frequently omitted from the methods. However, in most of the countries, the development of methods was still in progress to meet the WFD requirement. Definition of reference condition is a central component of all WFD compliant assessment tools but this is a challenge particularly in the assessment of hydromorphological alteration of reservoirs. Similarly, demonstrating strong links between hydromorphological indicators and biological quality elements remains a challenge with many knowledge gaps still evident. These results highlight the need for rapid collection of new environmental data and the need for conceptual and applied research to make methodological progress in assessing lake hydromorphology and ensuring habitat quality.

Ecosystem vulnerability is crucial information for conservation managers. We assessed the sensitivity and resilience (vulnerability components) patterns of fish and phytoplankton assemblages in French lakes (natural and artificial). We measured resilience (functional redundancy) and sensitivity, an index considering three characteristics of rarity for species. We hypothesized that geographically close lakes have similar resilience and sensitivity for fish assemblages (H1). Then, we tested the correlation between environmental gradients and resilience and sensitivity components, assuming that fish and phytoplankton do not respond similarly to environmental factors and that, consequently, there is no congruence between sensitivity and resilience patterns between of two groups. Also, we tested the hypotheses that species-rich assemblages show higher resilience and sensitivity in French lakes (H2); the highest values of resilience and sensitivity are related to phytoplankton (H3); and assemblages from natural lakes have higher resilience and sensitivity level (H4). We found similar resilience levels in spatially close fish assemblages due to fish dispersal limitations that contributed to create regional patterns in functional structure. Besides, acidity and eutrophication processes are good indicators of sensitivity level for fish. There is a mismatch in resilience and sensitivity levels between fish and phytoplankton, reinforcing importance of using a multi-taxa approach. Also, the components were positively related to taxonomic richness in assemblages showing importance of conserving biodiversity. Finally, we observed higher values of resilience and sensitivity for phytoplankton, as expected for a highly diverse group. Additionally, phytoplankton assemblages in natural lakes showed higher resilience levels than artificial environments, confirming the importance of preserving natural systems to conserve ecosystem functionality.

1. Hydromorphology provides a physical framework for aquatic biocenoses. Its condition directly affects the quality of habitats available for fauna and flora and its assessment is therefore required by the EU Water Framework Directive (WFD) to assess the ecological status of lake water bodies. 2. In this study, we developed an index of Lake HYdroMOrphology (LHYMO) to provide a quantitative assessment of the hydromorphological status of natural and non-natural lakes that can be used for the implementation of the WFD and is consistent with CEN standards. 3. This new index addresses the shortage of methods describing adequately hydromorphological alterations on lakes on both hydrology and morphology. LHYMO includes nine metrics related to morphological WFD quality elements (QE) and six metrics related to hydrological WFD QE, all of which considered to support biological elements. The reference conditions were defined for each metric using an original approach: the degree of alteration is measured in relation to the natural characteristics of each lake, relative to a state that ‘would be expected in the absence of disturbances’. 4. Besides its use for regulatory purposes, this index is also an interesting tool to monitor the efficacy of hydromorphological restoration projects or to help target effective conservation measures on lakes.5. Application of this index to 72 French lakes provides the first quantitative and homogeneous assessment of the hydromorphological quality of lakes over a whole territory and gives the first overview of the hydromorphological status of lakes in France, with classification into five classes ranging from ‘high’ to ‘bad’. 6. LHYMO is already operational for large French lakes as it relies mostly on reference datasets available at a national scale, and may also be used in a wider scope through gathering or completing data from other sources.

Assessing the vulnerability of ecosystems to biodiversity loss has become increasingly crucial in conservation and ecology research. This study proposed a methodology for measuring lake vulnerability to biodiversity loss employing an established framework that combines three components. For this, we measured the resilience (functional redundancy) and sensitivity (an index considering three characteristics of rarity) components for fish and phytoplankton communities. We also measured the exposure component of the main stressors in lakes. We then combined the three components and calculated the vulnerability index (IVCLA) using data from 255 French lakes. We found that all lakes exhibited low levels of resilience, elevated sensitivity regarding average values for fish and phytoplankton groups, and medium exposure to stressors associated with human activities. In addition, there were some discrepancies in resilience and sensitivity patterns between fish and phytoplankton groups, emphasizing the importance of considering information from multiple biological groups when assessing ecosystem vulnerability. Hydrological alterations and low water quality were key stressors related to higher lake vulnerability. Most French lakes have been classified as exhibiting moderate vulnerability. It is crucial to emphasize the potential increase in exposure risks, which could lead to even higher vulnerability levels and, subsequently, biodiversity loss in the future. The IVCLA index offers several advantages, including integrating multiple taxa groups and stressors. We recommend incorporating additional data, such as the resilience and sensitivity of the entire food web, and considering temporal responses to stressors to improve accuracy and predictive power. The IVCLA was developed with the purpose of serving as an effective tool for guiding environmental managers in designing conservation strategies and making informed decisions for lake ecosystems.

Introduction: Characterizing the thermal habitat of fish is key to understanding their ecological requirements in order to make appropriate management plans for the preservation of fish populations in the context of climate change. Little is known about the thermal habitat of the early life stages of fish (larvae and juveniles), as most methods have been designed for large, easily handled individuals. In particular, the study of otoliths holds great promise for unveiling the early thermal history of fish, although it is challenging to implement due to the very small size of the biological material.Methods: The stable oxygen isotope content (δ18O) of biogenic carbonates (such as otoliths) can be used to reconstruct the life temperature of fish individuals. However, relationships between δ18O of otoliths and ambient temperature are scarce and mainly developed for commercial species. In this study, we assessed the δ18O of juvenile European chub (Squalius cephalus, Linnaeus 1758) living in a section of the lower Rhône River in France.Results: The δ18O of otoliths showed significant relationship with ambient temperature [δ18Ooto(VPDB)- δ18Ow(VPDB) = 33.391 – 0.2641 * T (°C)], and the relationship between temperature and the fractionation factor (α) was 1,000 ln α = −43.472 + 21.205 [1,000/T(K)].Discussion: As expected, back-calculated temperatures from these equations were in much better agreement with the measured in situ temperatures than previously published equations. This equation is the first to be developed for leuciscid fish in Europe and the second in the world.