-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.

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Summary 1. Sediment plays a key role in internal nutrient cycling and eutrophication in lakes. However, studies focusing on the efficiency of the biomanipulation techniques for improving the control of primary producers have rarely examined the effects of changes in food‐web structure on the sediment biochemical composition and biodegradability. 2. In a 1‐year experiment conducted in large replicated mesocosms, we tested how the absence or presence of a zooplanktivorous fish (roach, Rutilus rutilus) affected the elemental composition and the potential biodegradability of recently deposited sediment in a eutrophic system. The potential biodegradability of these sediments was assessed in laboratory microcosms by measuring the production of CO2 during 44‐day incubations. 3. The potential biodegradability of recently deposited sediment from the fish treatment was 60% higher than that from the fishless treatment. This higher biodegradability was corroborated by a higher annual loss of sediment in fish enclosures (36%) than in fishless ones (16%). Annual losses of carbon, nitrogen and organic phosphorous were higher for sediment from fish enclosures. 4. Carbon and nitrogen contents of sediment were higher for the fish treatment. In contrast, the sediment C/N ratio, one of the proxies used to estimate sediment biodegradability, did not differ between treatments. No relationship was observed between elemental composition of sediment and its potential biodegradability. This latter appeared to be more probably dependent on the biochemical composition of the sediment and especially on the content of labile compounds such as proteins, sugars and polyunsaturated fatty acids. The use of sterols as biomarkers revealed an important degradation by microorganisms of 1‐year‐old sediment from both fish and fishless treatments. 5. Our results revealed that fish biomanipulations might favour clear water states not only through a stronger top–down control on phytoplankton but also through a lower biodegradability of sediment reducing internal nutrient cycling.