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SUMMARY1. Relationships between the assemblage structure of stygobionts (i.e. obligate groundwater species) and habitat conditions in aquifers were explored in the French Jura based on 16 environmental variables and presence ⁄ absence data on stygobiotic species. The two data sets were simultaneously collected at a total of 269 sites. 2. The study aimed to (i) identify the environmental factors determining the composition of stygobiotic assemblages at the regional scale; (ii) define the ecological preferences of the collected stygobiotic species along environmental gradients; and (iii) describe species assemblages occurring in similar habitats. These aims were pursued with a view to refine approaches to groundwater biodiversity assessment and sampling strategies. 3. A large number of stygobionts (62 species) were collected using a stratified sampling design. The measured environmental variables explained 72% of the overall variability in stygobiotic assemblage structure. Determining factors were primarily geology (pore size) and dissolved oxygen concentration, and secondarily altitude and distance of sampling sites from areas glaciated during the Pleistocene. Water chemistry and landcover variables had little influence on the composition of stygobiotic assemblages. 4. Ecological preferences of stygobiotic species were bounded along environmental gradients using Outlying Mean Index (OMI) analysis. Apart from rare species (frequency < 0.01), most stygobionts had a tolerance index >1, but residual tolerance observed in the most widespread species indicates sensitivity to other variables than those studied. 5. Biodiversity hotspots mainly occurred in highly permeable geological formations such as karst and coarse alluvial environments with well oxygenated water situated between 200 and 500 m altitude. More intensive sampling of high-altitude sites is unlikely to yield additional species, but rare species may be found at low and mid altitudes and at sites far from the Wü rm glaciers.

-Fifty years after the hyporheic zone was first defined (Orghidan, 1959), there are still gaps in the knowledge regarding the role of biodiversity in hyporheic processes. First, some methodological questions remained unanswered regarding the interactions between biodiversity and physical processes, both for the study of habitat characteristics and interactions at different scales. Furthermore, many questions remain to be addressed to help inform our understanding of invertebrate community dynamics, especially regarding the trophic niches of organisms, the functional groups present within sediment, and their temporal changes. Understanding microbial community dynamics would require investigations about their relationship with the physical characteristics of the sediment, their diversity, their relationship with metabolic pathways, their interactions with invertebrates, and their response to environmental stress. Another fundamental research question is that of the importance of the hyporheic zone in the global metabolism of the river, which must be explored in relation to organic matter recycling, the effects of disturbances, and the degradation of contaminants. Finally, the application of this knowledge requires the development of methods for the estimation of hydrological exchanges, especially for the management of sediment clogging, the optimization of self-purification, and the integration of climate change in environmental policies. The development of descriptors of hyporheic *Corresponding author: pierre.marmonier@univ-lyon1.frArticle published by EDP Sciences Ann. Limnol. -Int. J. Lim. 48 (2012) [253][254][255][256][257][258][259][260][261][262][263][264][265][266] Available online at: Ó EDP Sciences, 2012 www.limnology-journal.org DOI: 10.1051/limn/2012009 zone health and of new metrology is also crucial to include specific targets in water policies for the long-term management of the system and a clear evaluation of restoration strategies.