A cost-effective method to quantify biological surface sediment reworking

We propose a simple and inexpensive method to determine the rate and pattern of surface sediment reworking by benthic organisms. Unlike many existing methods commonly used in bioturbation studies, which usually require sediment sampling, our approach is fully non-destructive and is well suited for investigating non-cohesive fine sediments in streams and rivers. Optical tracer (e.g., luminophores or coloured sand) disappearance or appearance is assessed through time based on optical quantification of surfaces occupied by tracers. Data are used to calculate surface sediment reworking (SSR) coefficients depicting bioturbation intensities. Using this method, we evaluated reworking activity of stream organisms (three benthic invertebrates and a fish) in laboratory microcosms mimicking pool habitats or directly in the field within arenas set in depositional zones. Our method was sensitive enough to measure SSR as low as 0.2 cm2.d-1, such as triggered by intermediate density (774 m-2) of Gammarus fossarum (Amphipoda) in microcosms. In contrast, complex invertebrate community in the field and a fish (Barbatula barabatula) in laboratory microcosms were found to yield to excessively high SSR (>60 cm2.d-1). Lastly, we suggest that images acquired during experiments can be used for qualitative evaluation of species-specific effects on sediment distribution

Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses

[Departement_IRSTEA]EauxInternational audienceThe Pyrenean desman, a threatened, semiaquatic mammal, is considered a specialist predator feeding on aquatic benthic invertebrates. This categorization comes from visual identification of prey in scat or gut contents, often based on a limited number of samples and locations. We combined diet analyses using next-generation sequencing methods with an extensive survey to explore the summer diet of Pyrenean desmans across the French Pyrenees. This study thus provides an unprecedented level of detail on the trophic ecology of Pyrenean desmans. Our results revealed a diverse diet containing a high proportion of rare prey and substantial consumption of terrestrial prey, which suggests a more generalist diet than previously understood. Three diet groups were identified, with significant differences in prey composition. These differences were not related to geographic location, but rather to local environmental variables. The spatial variation in diet was likely induced by local abiotic parameters that affect prey availability or use of foraging habitats

Integrating hydrological features and genetically validated occurrence data in occupancy modeling of an endemic and endangered semi-aquatic mammal species, Galemys pyrenaicus, in a Pyrenean catchment

As freshwater habitats are among the most endangered, there is an urgent need to identify critical areas for conservation, especially those that are home to endangered species. The Pyrenean desman (Galemys pyrenaicus) is a semi-aquatic mammal whose basic ecological requirements are largely unknown, hindering adequate conservation planning even though it is considered as a threatened species. Species distribution modelling is challenging for freshwater species. Indeed, the complexity of aquatic ecosystems (e.g., linear and hierarchical ordering) must be taken into account as well as imperfect sampling. High-quality and relevant hydrological descriptors should also be used. To understand the influence of environmental covariates on the occupancy and detection of the Pyrenean desman, we combine both a robust sign-survey data set (i.e. with genetic validation ensuring true presence information) and a hydrological model to simulate the flow regime across a whole catchment. Markovian site-occupancy analysis, taking into account sign detection and based on spatially adjacent replicates, indicated a positive influence of heterogeneity of substrate and shelters, and a negative influence of flow variability on Pyrenean desman detection. This valuable information should help to improve monitoring programs for this endangered species. Our results also highlighted a spatially clustered distribution and a positive influence of stream flow and number of tributaries on occupancy. Hence, modifications of flow regime (e.g. hydropower production, irrigation, climate change) and habitat fragmentation appear to be major threats for this species, altering the connectivity between tributaries and the mainstream river as well as between adjacent sub-catchments

Potential impacts of climate change on the distribution of freshwater fishes in French streams and uncertainty of projections

Les changements climatiques et leurs impacts sur la biodiversité font aujourd'hui l'objet d'une attention croissante de la part de la communauté scientifique et des gestionnaires des écosystèmes naturels. En effet, le climat influence la biologie et l'écologie des espèces animales et végétales, depuis leur physiologie jusqu'à leur répartition. Les modifications climatiques pourraient donc avoir des répercussions importantes sur les espèces et les assemblages. Au sein des écosystèmes aquatiques continentaux, les poissons de rivière sont des organismes incapables de réguler leur température corporelle et soumis à une variabilité hydrologique importante ainsi qu'à de fortes pressions anthropiques. Leur réponse aux modifications du climat actuelles et à venir a pourtant été encore peu abordée. L'objectif de ce travail de thèse est donc d'évaluer les impacts potentiels du changement climatique sur les poissons des rivières françaises, et plus particulièrement sur la distribution des espèces et la structure des assemblages. Des données fournies par l'Office National de l'Eau et des Milieux Aquatiques ainsi qu'une approche de modélisation basée sur les niches écologiques des espèces (i.e., modèles de distribution) ont été utilisées. Différentes sources d'incertitude ont également été testées dans une approche d'ensembles afin de prendre en compte la variabilité entre les impacts projetés et fournir ainsi une évaluation robuste de ces impacts. La première partie de ce travail a consisté en l'identification des principaux déterminants environnementaux qui structurent la répartition spatiale des espèces de poisson au sein des réseaux hydrographiques. Globalement, il apparaît qu'une combinaison de facteurs climatiques et de variables décrivant l'habitat local et la position des habitats au sein des réseaux hydrographiques est importante pour expliquer la distribution actuelle des espèces. De plus, les espèces ont toutes des réponses différentes aux facteurs de l'environnement. Dans un second temps, nous avons mis en évidence que le choix de la méthode statistique de modélisation de la niche écologique est crucial, les patrons actuels et futurs de distribution prédits étant fortement contrastés selon la méthode de modélisation considérée. Cette dernière s'avère même être la principale source d'incertitude dans les projections futures, bien plus encore que les modèles climatiques de circulation générale et les scénarios d'émission de gaz à effet de serre. La variabilité entre les prédictions issues de plusieurs techniques de modélisation peut être prise en compte par une approche de consensus. Un modèle consensuel basé sur la valeur moyenne de l'ensemble de prédictions est capable de prédire correctement la distribution actuelle des espèces et la composition des assemblages. Nous avons donc choisi de retenir cette approche pour évaluer au mieux les impacts potentiels du changement climatique sur les poissons des rivières françaises à la fin du 21ème siècle. Nous avons montré que la majorité des espèces de poisson pourrait être affectée par les futures modifications du climat. Seules quelques espèces d'eau froide (e.g. truite fario, chabot) pourraient restreindre leur distribution aux parties les plus apicales des réseaux hydrographiques. Au contraire, les espèces tolérant des températures plus élevées pourraient coloniser de nouveaux habitats et étendre ainsi leur répartition. Ces modifications de la distribution des espèces pourraient conduire à un réarrangement des assemblages au niveau taxonomique et fonctionnel. Une augmentation de la diversité locale et de la similarité régionale (i.e., homogénéisation) sont ainsi prédites simultanément. L'ensemble de ces résultats apporte donc des éléments sur la compréhension de la distribution des poissons d'eau douce et sur les conséquences du changement climatique qui peuvent être envisagées. Ce travail fournit ainsi une base aux acteurs de la gestion de la biodiversité afin d'initier des mesures de conservation concrètes. De plus, les considérations méthodologiques développées dans cette thèse sont une contribution importante à l'amélioration des projections issues de modèles statistiques de distribution et à la quantification de leur incertitude.Climate change and its impact on biodiversity are receiving increasing attention from scientists and people managing natural ecosystems. Indeed, climate has a major influence on the biology and ecology of fauna and flora, from physiology to distribution. Climate change may thus have major consequences on species and assemblages. Among freshwater ecosystems, stream fish have no physiological ability to regulate their body temperature and they have to cope with streams' hydrological variability and strong anthropogenic pressures. Yet their response to current and future climate change has been poorly studied. The aim of this PhD thesis is to assess the potential impact of climate change on fish in French streams, mainly on species distribution and assemblages' structure. Data provided by the Office National de l'Eau et des Milieux Aquatiques combined with a modelling approach based on species' ecological niche (i.e., distribution models) have been used. Several sources of uncertainty have also been considered in an ensemble modeling framework in order to account for the variability between projected impacts and to provide reliable estimates of such impact. First, we have identified the main environmental factors that determine the spatial distribution of fish species within river networks. Overall, it appears that a combination of both climatic variables and variables describing the local habitat and its position within the river network is important to explain the current species distribution. Moreover, each fish species responded differently to the environmental factors. Second, we have highlighted that the choice of the statistical method used to model the fish ecological niche is crucial given that the current and future patterns of distribution predicted by different statistical methods vary significantly. The statistical method appears to be the main source of uncertainty, resulting in more variability in projections than the global circulation models and greenhouse gas emission scenarios. The variability between predictions from several statistical methods can be taken into account by a consensus approach. Consensual predictions based on the computation of the average of the whole predictions ensemble have achieved accurate predictions of the current species distribution and assemblages' composition. We have therefore selected this approach to assess the potential impacts of climate change on fish in French streams at the end of the 21st century with the highest degree of confidence. We have found that most fish species could be sensitive to the future climate modifications. Only a few cold-water species (i.e., brown trout, bullhead) could restrict their distribution to the most upstream parts of river networks. On the contrary, cool- and warm-water fish species could colonize many newly suitable habitats and expand strongly their distribution. These changes of species distribution could lead to a rearrangement of fish assemblages both at the taxonomic and functional levels. An increase in local diversity together with an increase in regional similarity (i.e., homogenization) are therefore expected. All these results bring new insights for the understanding of stream fish species distribution and expected consequences of climate change. This work thus provides biodiversity managers and conservationists with a basis to take efficient preservation measures. In addition, methodological developments considered in this PhD thesis are an important contribution to the improvements of projections by statistical models of species distribution and to the quantification of their uncertainty

Hindcasting modelling for restoration and conservation planning: application to stream fish assemblages

International audienceAlthough ecosystems are increasingly threatened worldwide, the resources available to set up management actions, such as conservation or restoration, remain severely limited. Methods designed to spatially allocate conservation and restoration actions while maximizing their ecological benefits are urgently needed. Whereas conservation planning methods have been extensively developed in past decades, improvements in restoration planning are still needed to build efficient management tools. This methodological gap may be explained by the difficulties encountered when estimating non-disturbed ecological conditions (i.e. reference conditions) which are usually required to compare past and present ecosystem states. Here, the species composition of stream fish assemblages in 607 river stretches of the Pas-de-Calais department in the north of France was predicted using species distribution models. Present occurrence was predicted according to four environmental variables, including two related to human-induced disturbances (i.e. proportion of river stretch length affected by hydraulic works and local geomorphological alterations). The fish assemblages potentially present in the absence of such disturbances were then predicted using hindcasting modelling which involves artificially setting to zero the values of the disturbance variables in the models.A framework based on a multi-faceted approach of diversity was applied to the present-day fish assemblages and those predicted under the two non-disturbed scenarios (i.e. restoration scenarios) to assess their suitability for management. While the theoretical restoration of the natural flow regimes was likely to result in few changes in fish assemblage composition and consequently in their multi-faceted diversity, the restoration of natural geomorphological characteristics was predicted to reduce the taxonomic diversity but increase the functional diversity, the natural heritage importance and the socioeconomic value of the fish assemblages.This study provides environmental decision-makers with a tool to identify precisely and simultaneously the conservation and restoration actions that have to be undertaken as a priority, by comparing the present and non-disturbed multi-faceted diversity indices

Combining expert‐based and computational approaches to design protected river networks under climate change

International audienceAim: Estimate the current and future distribution of brown trout and identify priority areas for conservation of the species.Location: Rhône River basin and Mediterranean streams.Methods: We first developed a spatially explicit species distribution model to es- timate the current and future distribution of brown trout for three time horizons (2030, 2055 and 2080) and two climate change scenarios (RCP 4.5 and RCP 8.5). We then performed a prioritization analysis to identify priority areas for brown trout conservation, accounting for: (a) spatial dependencies along the riverine system, (b) several sources of uncertainty arising from climate-related forecasts and (c) different protected area scenarios by comparing hypothetical, optimal protected networks to an actual protected network designed by regional fish experts.Results: Future projections of brown trout densities exhibited a general trend to- wards a gradual range contraction, with a significant risk of extirpation across moun- tainous regions of low to mid-elevation. Overall, the projected current and future distributions were well-covered by the existing protected network. In addition, up to 70% of the river reaches included in this expert-based protection network were also priorities in the optimal priority set (e.g. the best set of areas to maximize biodiversity protection). Finally, a large proportion of these reaches were invariably identified re- gardless of climate change scenarios and uncertainties or spatial dependencies. Main conclusions: Our analytical approach highlighted priority areas for brown trout conservation which were robust to a set of climate and connectivity assumptions. This core priority network could be further refined by taking into account key fine- scale processes like thermal refugia. Therefore, we advocate for combining computa- tional and expert-based approaches in conservation planning of riverine ecosystems to achieve a relevant consensus between regional-scale management and fine-grain ecological knowledge

Detection and Monitoring of Riverine Dragonfly of Community Interest (Insecta: Odonata): Proposal for a Standardised Protocol Based on Exuviae Collection

Collecting quantitative data on insect species occurrence and abundance is a major concern to document population trends. This is especially the case to assess the conservation status of species listed in the European Habitats Directive and to assess the efficiency of mitigation measures with a view to achieve the “no net loss of biodiversity” goal for protected species. However, at present, populations of riverine dragonflies listed in the Habitats Directive and protected under French national law are poorly quantified and monitored. Exuviae collection could be used for such monitoring but a standardised protocol is lacking. We here proposed and tested such a protocol to monitor riverine dragonfly populations through exhaustive exuviae collection along river bank transects. To define the optimal transect size and number of visits, ninety-eight 100 m-long transects divided into 10 m-long plots were monitored on three rivers in southern France. Each transect was visited three times over the emergence period. In the course of each visit, all the exuviae along transects were collected and identified. From our results, we recommend collecting exuviae along 100 m of river bank in the course of two visits in order to both maximise the species detection and minimise the monitoring cost