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This chapter presents the causes of physical and ecological degradation of estuaries in relation to human activities and climate change. The direct and indirect effects of degradation on ecosystem services and fish are listed, as well as the key questions that need to be answered in order to undertake rehabilitation and restoration actions. Ecohydrology and ecoengineering are indispensable tools to be mobilised alongside a variety of models to guide actions in favour of habitat and whole estuary functioning. Finally, several examples of restoration are presented to move from theory to practice. The restoration of estuaries has often become essential to ensure sustainable fish communities and requires a holistic view of the problems and a coordination of efforts to ensure the success of the actions undertaken.

International audience; 1. The hyporheic zone of rivers potentially acts as a dispersal corridor for ground-water organisms because it provides a spatially continuous interstitial habitat between isolated aquifers. Yet, the degree to which it can facilitate the move- ment of organisms has been hypothesized to vary in response to change in sedi- ment regime, which determines channel morphology.2. In this study, we used microsatellite markers to test for a relationship between the genetic structure and diversity of the minute interstitial isopod Proasellus walteri and channel morphology along three nearby hyporheic corridors differing widely in their sediment regime. We predicted that genetic diversity would decrease and genetic structuring would increase as sediment supply-limited channels would become prominent features in the river corridor. The reason is that such channels have fewer and less suitable sedimentary habitats for migra- tion because they lack large depositional bedforms such as gravel bars.3. Using genotypic data from seven microsatellite loci for a total of 713 individuals distributed among 25 demes, we found that demes had on average more alleles and were less differentiated in the river showing the most extensive alluvial depos- its and shortest length of sediment supply-limited channels. Population clusters were also of greater size, reaching up to 30 km in length. The longitudinal pattern of genetic differentiation in this sediment-rich river was best explained by hydro- logic distance and the longitudinal pattern of allelic richness was bell-shaped, as expected under a stepping-stone model with symmetrical migration.4. The length of sediment supply-channels was more important than hydrologic dis- tance in explaining the longitudinal distribution of genetic differentiation in the two other corridors facing a sediment shortage. Allelic richness decreased mono- tonically upstream in the most sediment-poor river. This correlates with the expan- sion further downstream of sediment supply-limited channels in this river, which is likely to decrease animal movement and hence gene flow among demes.5. Thisstudyprovidesthefirstevidencethatthedegreetowhichthehyporheiczone facilitates the movement of groundwater organisms varies greatly among rivers of contrasted geomorphology. Extending the application of riverscape genetics across a range of interstitial taxa and geomorphic settings holds much promise for assessing the contribution of the hyporheic zone to the dispersal of groundwater organisms.

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE; International audience; River landscapes are increasingly viewed as a collection of nested geomorphic features, the hydrological effects of which juxtapose to create a mosaic of aquatic habitat conditions. We examined how the combined hydrological influences of stream reaches and gravel bars affect the composition of hyporheic invertebrate assemblages along the longitudinal and vertical dimensions of river landscapes. We worked in 12 braided-river valley segments of tributaries to the Rhone River, France. Valley segments were bounded downstream by geological knickpoints so that bedform-induced exchange flows beneath gravel bars and riffles were predictably embedded in exchange flows occurring at the valley-segment scale. In upstream reaches (UR) and downstream reaches (DR) of each valley segment, we collected invertebrates at the heads and tails of gravel bars in the hyporheic zone and at the upstream and downstream ends of riffles in surface channels adjacent to the bars. Patterns of vertical hydraulic gradient and specific conductance and the resulting spatial heterogeneity of temperature, dissolved O-2, and particulate organic C suggested that DR were points of flow convergence and water mixing. Specific conductance increased and temperature decreased more steeply along gravel bars in DR, indicating that water from long hyporheic flow paths or lateral aquifers was discharging at the tails of bars in DR. Density hotspots for insect larvae corresponded to hyporheic patches at the heads of bars in DR, which received the highest organic matter inputs from localized downwelling of surface water and were not affected by inputs of cold water from hyporheic flow paths or lateral aquifers. Density of epigean taxa at the tails of bars decreased more steeply with depth in DR than in UR, and density of hypogean taxa increased more steeply. Viewing local hyporheic assemblages as the outcome of a series of environmental filters operating over multiple exchange flows induced by nested geomorphic features provides a general framework that may foster our understanding of biodiversity patterns in river landscapes.

International audience; Effective population size (Ne) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of Ne in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small Ne. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proasellus walteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for Ne estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that Ne in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small Ne.