Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Streambed substrates have pervasive effects on stream biodiversity and biogeochemistry. The excessive input of fine sediments in streams and the subsequent alteration of the physical characteristics of streambed substrates are considered today as a major environmental issue. The estimation of streambed hydraulic conductivity (K) may be simpler than other estimations of reach-scale physical characteristics and could serve to quantify the alterations of streambeds across stream networks. In this study, we examined between-reach and within-reach variability and temporal changes of streambed K across 101 stream reaches in France, including nine reaches previously judged as clogged and nine as references (unclogged). We also examined the relationships between K and some environmental variables such as vertical hydraulic gradient, streambed grain size, flow velocity or distance to the bank. We demonstrated that 15 measurements of streambed K per reach could be used to compare streams among each other and over time. Clogged reaches displayed much lower K than reference reaches, and more generally, reach-averaged K and the number of non-null K values per reach allowed discriminating reaches among each other without observer bias. K was higher in upwelling compared with downwelling areas, probably because of fine sediment uplifting. With the low cost in terms of equipment (<€100 per unit) and time (2-4 h per site), reach-scale streambed K estimates are promising for studying the alterations of streambed substrates across stream monitoring networks such as clogging, but also for understanding large-scale drivers of these alterations, or for upscaling recent developments in hyporheic ecology at the reach scale.

Aquatic hyphomycetes play an essential role in the decomposition of allochthonous organic matter which is a fundamental process driving the functioning of forested headwater streams. We studied the effect of anthropogenic acidification on aquatic hyphomycetes associated with decaying leaves of Fagus sylvatica in six forested headwater streams (pH range, 4.3-7.1). Non-metric multidimensional scaling revealed marked differences in aquatic hyphomycete assemblages between acidified and reference streams. We found strong relationships between aquatic hyphomycete richness and mean Al concentration (r = -0.998, p < 0.0001) and mean pH (r = 0.962, p < 0.002), meaning that fungal diversity was severely depleted in acidified streams. By contrast, mean fungal biomass was not related to acidity. Leaf breakdown rate was drastically reduced under acidic conditions raising the issue of whether the functioning of headwater ecosystems could be impaired by a loss of aquatic hyphomycete species.

-Knowledge on ecological impacts of forestry practices on aquatic ecosystems relies almost exclusively on data from large-scale forest harvesting, often involving clearfelling of whole stream catchments. To determine effects associated with less intensive and widespread forest management, we examined the responses of headwater streams to small-scale forest harvesting, including riparian zones adjacent to study reaches but corresponding to less than 5% of the catchment areas. Stream reaches running through recently (2-4 years) harvested forest patches were paired with and compared with adjacent reaches bordered by mature broadleaf forest. We determined abiotic stream characteristics, invertebrate community structures and abundances, trout size and population densities, and leaf litter breakdown rates in each of these pairs. Harvested reaches were found to have different channel cross-section morphology and greater invertebrate abundances in leaf packs than mature forest reaches. Shifts in the abundance of common invertebrate predators were also attributed to riparian forest harvesting. Litter breakdown rates and brown trout densities did not show any significant difference between harvested and mature forest reaches across the four site pairs, possibly because of nonlinear responses to post-harvest riparian canopy openness. Managers must be aware that small-scale forest harvesting in stream riparian areas is not without consequences for aquatic ecosystems. Whether natural riparian forest openings, such as caused by tree death and blow-down, have similar effects on stream ecosystems is an important question to address if we are to confirm the usefulness of small-scale forestry and improve forest and stream management schemes.

1. Headwater stream ecosystems are primarily heterotrophic, with allochthonous organic matter being the dominant energy. However, sunlight indirectly influences ecosystem structure and functioning, affecting microbial and invertebrate consumers and, ultimately, leaf litter breakdown. We tested the effects of artificial shading on litter breakdown rates in an open-canopy stream (high ambient light) and a closed-canopy stream (low ambient light). We further examined the responses of invertebrate shredders and aquatic hyphomycetes to shading to disentangle the underlying effects of light availability on litter breakdown. 2. Litter breakdown was substantially slower for both fast-decomposing (alder, Alnus glutinosa) and slow-decomposing (beech, Fagus sylvatica) leaf litters in artificially shaded stream reaches relative to control (no artificial shading) reaches, regardless of stream type (open or closed canopy). 3. Shredder densities were higher on A. glutinosa than on F. sylvatica litter, and shading had a greater effect on reducing shredder densities associated with A. glutinosa than those associated with F. sylvatica litter in both stream types. Fungal biomass was also negatively affected by shading. Results suggest that the effects of light availability on litter breakdown rates are mediated by resource quality and consumer density. 4. Results from feeding experiments, where A. glutinosa litter incubated under ambient light or artificial shade was offered to the shredder Gammarus fossarum, suggest that experimental shading and riparian canopy openness influenced litter palatability interactively. Rates of litter consumption by G. fossarum were decreased by experimental shading in the open-canopy stream only. 5. The results suggest that even small variations in light availability in streams can mediate substantial within-stream heterogeneity in litter breakdown. This study provides further evidence that changes in riparian vegetation, and thus light availability, influence organic matter processing in heterotrophic stream ecosystems through multiple trophic levels.