Key recent publications

New Book: Intermittent Rivers and Ephemeral Streams. Editors: Thibault Datry Núria Bonada Andrew Boulton
eBook ISBN:9780128039045/ Paperback ISBN:9780128038352



Special Issues:

Special Issue River Research and Applications: Ecohydraulics, 2017. Ecohydraulics from microhabitats to catchment management.
Guest Editors : Harby A., Lamouroux N., Martinez-Capel F.

 Special Issue Journal of Environmental Management: Large-scale river management: 2017. Enlarging spatial and temporal scales for riverine biophysical diagnosis and adaptive management.
Guest Editors : Piégay H., Lamouroux N.

Special Issue Freshwater Biology: Intermittent Rivers Ecology, 2016. Intermittent river ecology as a maturing, multi-disciplinary science.
Guest Editors : Thibault Datry, Ken Fritz & Catherine Leigh

Special Issue Freshwater Biology: River Restoration, 2015. Towards a predictive restoration ecology: a case study of the French Rhône River
Guest Editors : Nicolas Lamouroux , James A. Gore, Fabio Lepori & Bernhard Statzner

Publication List  here

Latest publications

HAL : Dernières publications

  • [hal-04298245] Caractérisation des habitats piscicoles d’une rivière intermittente par imagerie drone

    La structuration morpho-écologique des cours d'eau est un des facteurs clefs de la répartition des habitats et implicitement de la qualité des milieux aquatiques fluviaux. Dans un contexte de réchauffement climatique global, ces milieux complexes et sensibles vont être de plus en plus concernés par des phénomènes d'assèchement partiel ou intégral de leur lit impactant les continuums écologiques piscicoles. Le besoin d'outils opérationnels est donc primordial pour étudier les variations physiques des tronçons de rivière et fournir des indicateurs caractérisant les méso-formes (seuils, mouilles, radiers, végétation rivulaire), leur répartition et leur suivi afin d'évaluer leur qualité. Le projet de recherche RIVERSIDE (Restitution du fractionnement des méso-habitats des rIVières intERmittenteS par Imagerie DronE) a pour objectifs, i) d'éprouver la capacité des données LiDAR et des images traitées par photogrammétrie à restituer les méso-formes des habitats, d'en extraire les caractéristiques physiques, iii) de croiser ces métriques avec les relevés piscicoles (inventaires localisés). (Jérôme Lejot) 21 Nov 2023
  • [hal-04313500] A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database

    Abstract Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species‐rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large‐scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade‐offs during groundwater colonization. (Nathanaelle Saclier) 23 Apr 2024
  • [hal-04313613] Spatiotemporal patterns of macroinvertebrate assemblages across mountain streams with contrasting thermal regimes

    Water temperature is recognized as an important driver of aquatic ecosystems and is of increasing interest because of global warming. However, to date, no studies have disentangled the contribution of annual thermal variability from the contributions of annual thermal mean and other environmental variables to spatiotemporal patterns of macroinvertebrate assemblages in mountain streams. In this study, we explored patterns of macroinvertebrate biodiversity within and among 5 mountain stream sites in the Serio watershed (Orobic Alps, Northern Italy) along a gradient of annual water thermal variability (annual range: ~1–16°C) but with similar means. At each site, macroinvertebrates were sampled; physicochemical variables, flood disturbance, and resource availability were measured monthly over a year; and water temperature was monitored continuously. The relationship between macroinvertebrate assemblages and environmental conditions was described by separating time and space through co-inertia analyses. Results showed a strong temporal co-inertia, with floods and mean monthly temperature most associated with within-site macroinvertebrate temporal patterns (70% of total variance) and with the greatest effects on the abundance of stoneflies. Synchronous floods occurred in all sites and promoted changes in macroinvertebrate community composition through a loss of taxa and individuals, whereas monthly water temperature variations were associated with the replacement of individuals among taxa. Spatial differences (30% of the total variance) were mainly linked to geographical proximity, although annual thermal variability covaried with annual temporal dissimilarity in taxonomic composition, suggesting that temporal patterns also explain spatial differences. Overall, the study indicates that even when accounting for the overall environmental setting, the thermal regime remains an important driver of macroinvertebrate spatiotemporal patterns. Mountain streams are particularly subject to thermal variation, and an increase in mean water temperature and thermal variability will substantially influence community composition, with the strongest effects on cold stenothermal taxa. Large-scale research across mountain ranges is essential to properly assess how spatiotemporal thermal heterogeneity influences the distribution of macroinvertebrates, as well as to guide conservation strategies in the context of increasing global warming. (Luca Bonacina) 29 Nov 2023
  • [hal-04318861] How low can you go? Widespread challenges in measuring low stream discharge and a path forward

    [...] (Erin Seybold) 02 Dec 2023
  • [hal-04313486] Environmental DNA complements scientific trawling in surveys of marine fish biodiversity

    Environment al DNA (eDNA) met abarcoding is a method to detect t axa from environment al samples. It is increasingly used f or marine biodiv ersity surv e y s. As it only requires water collection, eDNA metabarcoding is less in v asiv e than scientific trawling and might be more cost effective. Here, w e analy sed data from both sampling methods applied in the same scientific surv e y targeting Northeast Atlantic fish in the B a y of Biscay. We compared the methods regarding the distribution of taxonomic, phylogenetic, and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the tra wl, e v en though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on tra wling. Ho w e v er, consistency betw een abundance estimates pro vided b y eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is a promising method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence, but not yet for abundance. (Pierre Veron) 29 Nov 2023
  • [hal-04318862] A metasystem approach to designing environmental flows

    Abstract Accelerating the design and implementation of environmental flows (e-flows) is essential to curb the rapid, ongoing loss of freshwater biodiversity and the benefits it provides to people. However, the effectiveness of e-flow programs may be limited by a singular focus on ensuring adequate flow conditions at local sites, which overlooks the role of other ecological processes. Recent advances in metasystem ecology have shown that biodiversity patterns and ecosystem functions across river networks result from the interplay of local (environmental filtering and biotic interactions) and regional (dispersal) ecological processes. No guidelines currently exist to account for these processes in designing e-flows. We address this gap by providing a step-by-step operational framework that outlines how e-flows can be designed to conserve or restore metasystem dynamics. Our recommendations are relevant to diverse regulatory contexts and can improve e-flow outcomes even in basins with limited in situ data. (Mathis Messager) 02 Dec 2023
  • [hal-04198078] Recent trends in the chemistry of major northern rivers signal widespread Arctic change

    Rivers integrate processes occurring throughout their watersheds and aretherefore sentinels of change across broad spatial scales. River chemistryalso regulates ecosystem function across Earth’s land–ocean continuum,exerting control from the micro- (for example, local food web) to the macro-(for example, global carbon cycle) scale. In the rapidly warming Arctic, awide range of processes—from permafrost thaw to biological uptake andtransformation—might reasonably alter river water chemistry. Here weuse data from major rivers that collectively drain two-thirds of the ArcticOcean watershed to assess widespread change in biogeochemical functionwithin the pan-Arctic basin from 2003 to 2019. While the oceanward flux ofalkalinity and associated ions increased markedly over this time frame, nitrateand other inorganic nutrient fluxes declined. Fluxes of dissolved organiccarbon showed no overall trend. This divergence in response indicatesthe perturbation of multiple processes on land, with implications forbiogeochemical cycling in the coastal ocean. We anticipate that these findingswill facilitate refinement of conceptual and numerical models of currentand future functioning of Arctic coastal ecosystems and spur research onscale-dependent change across the river-integrated Arctic domain. (Suzanne Tank) 01 Feb 2024
  • [hal-04248122] The recovery of European freshwater biodiversity has come to a halt

    Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity. (Peter Haase) 23 Oct 2023
  • [hal-04177222] Do temperature and population size structure influence the quantity of fish eDNA in water?

    Various factors can influence the concentration of eDNA found in the environment and blur the link between eDNA results and in situ fish abundances, biomasses or even occurrences. We studied the influence of one abiotic factor, the temperature, and one biotic factor, the fish size class, on the amount of fish eDNA detectable in water. To do so, we conducted two controlled experiments using tench (Tinca tinca, L) placed into outdoor mesocosms during 1 week. The quantification of fish eDNA abundances was performed using quantitative PCR after filtrating a large volume of water (30 L). The Bayesian hierarchical ANOVAs performed on qPCR results did not detect the effect of size class on eDNA amount, but fish eDNA concentration was shown to increase significantly when temperature rose by 6 °C (no effect detected at 3 °C). This suggests that fish assemblage quantification of two thermally contrasting sites through eDNA is not directly comparable. (Alix Hervé) 04 Aug 2023
  • [hal-04182605] Past and future discharge and stream temperature at high spatial resolution in a large European basin (Loire basin, France)

    This paper presents retrospective simulations (1963-2019) and future projections (1976-2100) of daily time series of discharge and stream temperature for 52 278 reaches (median length of 1.3 km) over the Loire River basin (10 5 km 2) in France, using a physical process-based thermal model coupled with a semidistributed hydrological model. Retrospective simulations are based on the 8 km gridded Safran meteorological reanalysis over France. Twenty-first century projections are based on a subset of the 8 km gridded and bias-corrected DRIAS-2020 dataset over France. The discharge and stream temperature dataset stands out from existing ones thanks to its large scale and its high spatial resolution and the use of a physical processbased thermal model. The whole dataset is freely available and can be downloaded in NetCDF format from (Seyedhashemi et al., 2022a). (Hanieh Seyedhashemi) 17 Aug 2023
  • [hal-04178324] Comparing field, probabilistic, and 2D numerical approaches to assess gravel mobility in a gravel-bed river

    Sediment transport is a key process that affects the morphology and ecological habitat diversity of rivers. As part of a gravel augmentation program to mitigate sediment deficit below a dam, gravel mobility in the Ain River in Eastern France was investigated by tracking of a large amount (n = 1063) of PIT-tagged gravels in the field, conducting a probabilistic approach based on published tracer studies, and performing two-dimensional (2D) numerical modeling of flow and bedload transport. This study highlights the strengths, weaknesses, and complementary aspects of the three approaches to the understanding of river gravel mobility. Thanks to recent technological improvements, PIT-tagged gravels provide an increasingly reliable and accurate representation of the bedload movement in the field, although it remains limited in spatio-temporal resolution. Based on an exponential distribution, the probabilistic approach correctly reproduces the average trend in travel distances by the different classes of particles over hydrological periods, including one or several significant floods. The 2D numerical modeling accounts for the variability of local hydrodynamic conditions and can simulate realistic displacement distributions for the different classes of particles with high spatio-temporal resolution. Numerical modeling is a very encouraging approach, which makes our study original because it is the first time that the estimation of mean travel distances, the application of an exponential distribution, and the comparison with a hydrodynamic model are combined. A more effective modeling strategy involves incorporating a probabilistic transport model in the 2D numerical model to reproduce the observed scatter of the individual particle trajectories. (Fanny Arnaud) 07 Aug 2023
  • [hal-03368959] Coupling 3D hydraulic simulation and fish telemetry data to characterize the behavior of migrating smolts approaching a bypass

    Human-induced river fragmentation is a major threat to migratory fish species. Restoringriver connectivity requires the construction of fish passage solutions, such as fishways forupstream and downstream migration. While many studies focussed on the upstream migra-tion of diadromous fishes, and especially of adult Atlantic salmons (Salmosalar), we analyzejuvenile behaviour under different hydraulic conditions at reservoir to improve the develop-ment of effective bypass systems for downstream passage of salmon smolt.Based on coupling three-dimensional (3D) computational fluid dynamics (CFD) simulationsto smolt positions tracked by two-dimensional (2D) telemetry, the present study aimed toexplore smolt behaviour in relation to hydraulic cues. More specifically, we explored howhydraulic conditions influence fish behaviour and how fish navigate depending on thisbehaviour. In 2017, 23 smolts were tracked in the reservoir of Poutes (Allier River, France),associated with different turbine discharge rates. 3D CFD simulations were performed andvalidated against field measurements in the reservoir upstream of the hydropower plant.The study of fish displacements in relation to flow conditions provided new insights withthe use of thrust force, swimming orientation and direction as means to precisely character-ize smolt behaviour, which can help in the design of downstream migration passage facili-ties. At Poutes dam, flow velocity, flow acceleration and turbulent kinetic energy are verylow and therefore can lead to fish disorientation. However, results underlined that having aminimum flow velocity of 20cm/s in reservoirs is sufficient to prevent delay and allowfish navigation; (Noor Ben Jebria) 08 Sep 2023
  • [hal-04151628] Past and future joint trends in river temperature and flow: implications for diadromous fish

    Most key life-cycle events of organisms are synchronized by complex interactions of environmental cues to ensure optimal survival and growth of individuals and their offspring. However, this synchronicity is threatened by global change, which modifies the hydrological and thermal regimes of rivers worldwide. In particular, the asynchronous evolution of river temperature and flow can alter the duration and frequency of environmental windows suitable for the migration of diadromous fish. In this research project, we first developed the ‘Choc’ method to explore temporal CHanges in the OCcurrence of associations in bivariate time series. We applied this method to several case studies, which highlighted how global change has altered the conditions under which the endangered European eel and Atlantic salmon migrate, and how they have responded to these environmental changes. Recently, reconstructed (1963-2019) and projected (2020-2100) daily river temperature and flow data have been modelled over the entire hydrographic network of the Loire catchment (France). We combined this extensive dataset with daily fish passages available at fishways to assess the spatial and seasonal variability of trends in temperature-flow associations at a large scale. We then described how it has affected and will likely affect migration conditions of Atlantic salmon, allis shad and sea lamprey in the Loire catchment. Finally, we developed indicators to quantify past, present and future environmental suitability for their migration that allow comparison between rivers and tributaries, thereby providing operational results for the conservation of diadromous species and the prioritization of management actions in the context of global change. (Anthony Maire) 06 Jul 2023
  • [hal-04176046] Riparian vegetation mitigates river warming: exploring its large scale effects on past and future thermal regimes

    As air temperature increases worldwide due to climate change, stream temperature (Tw) is expected to follow a similar trajectory with even faster changes. In this study, we aimed at investigating and quantifying the extent to which riparian shading can help mitigate river warming at a large scale (105 km²). To do so, a physical process-based thermal model coupled with a semi-distributed hydrological model was used to reconstruct (1963-2019) and project (2005-2100) Tw for 52000 hydrographic sections of the Loire basin (France). This high spatial resolution (1 km) model includes a novel routine to account for riparian shading dynamically across seasons. Results showed that past and future increases in Tw were greater in relatively large rivers (Strahler order≥5), which was attributed partly to the mitigation effect of riparian shading observed on smaller streams. Indeed, riparian vegetation shading mitigated spring and summer Tw increases by up to 0.16°C per decade in headwater streams (i.e. < 30 km from the source) over the past six decades. Moreover, riparian shading could mitigate the future increase in summer Tw in small streams by 3.75°C to 5.17°C by the end of the 21st century, depending on the climate model and scenario from sparsely shaded reaches to highly shaded reaches. We complemented these results by exploring the consequences of theoretical scenarios of large-scale riparian restoration or loss on Tw changes. Our results suggest that the restoration and maintenance of riparian forests holds great promise to help mitigate the effects of global warming on rivers and their biodiversity. (Hanieh Seyedhashemi) 15 Aug 2023
  • [hal-04187405] SEINARIOS: Modelling river fish distribution under connectivity constraints

    Anthropogenic change and its effects on rivers cause fish to adapt through a shift in their distribution. However, the management of rivers leads to connectivity constraints (dams, sluices, etc.) which impede this dynamic. Our study sought to characterize connectivity’s influence on fish distribution. To do so, we worked on the extended Seine River basin (France), a heterogeneous, 95,000 square kilometer area that includes more than 14,000 artificial barriers. Our analyses relied on a unique dataset of fish species abundance for 52 species, covering 20 years and 2,200 stations. We first calculated connectivity metrics, often overlooked in this context, from species-specific leptokurtic dispersal kernels, using the R package {riverconn} to account for asymmetrical dispersal (upstream and downstream). Second, we built a set of species distribution models (SDM) to explain current fish distribution in relation to climatic and hydrological conditions and land use. Third, to assess the importance of connectivity in fish species distribution, our innovative approach was to include connectivity metrics in the SDMs and estimate the contribution of these metrics to model performance. Our results will contribute to a better understanding and quantification of the importance of connectivity in river fish distribution in anthropized environments. Furthermore, this work will allow predicting biodiversity under scenarios of global change and open doors for application to different catchments. (Swann Felin) 24 Aug 2023
  • [hal-04148822] Spatio-temporal dynamics of habitat use by fish in a restored alluvial floodplain over two decades

    Floodplain channels of rivers can serve as reproduction, nursery or refuge areas for fish. Although the complementary use of floodplain and main channels is known, few studies attempted to quantify this use and even fewer analysed its controlling factors. The objectives of this study are (1) to describe the spatio-temporal use of floodplain habitats and to identify their roles as complementary habitats for fish and (2) to analyse how abiotic variations and their modifications under restoration impact habitat use by fish. To meet these objectives, we analysed multi-site data collected over 20 years in eight restored sectors of the Rhône River. Results show that habitat use by fish is mainly related to spatial effects. As expected, rheophilic species were more abundant in lotic stations and limnophilic species in lentic ones. In addition, we identified an euryecious guild, grouping youngs of the year taxa, that used all types of habitats and particularly lentic floodplain channels with short life-span. Temporal effects combine (1) the effect of restoration, particularly in floodplain channels for which the connectivity regime was modified, (2) the effect of high flows upon the habitat use by fish that reinforces the nursery and refuge functions of floodplain channels. To conclude, our results demonstrate the importance of restoring habitat diversity and connectivity because habitats may have complementary functions for fish. Furthermore, our results also highlight that it is essential to account for temporal variations in order to better estimate the potential effects of restoration on river and their floodplains. (Anaëlle Bouloy) 03 Jul 2023
  • [hal-04148814] Past and future joint trends in river temperature and flow: implications for diadromous fish

    Most key life-cycle events of organisms are synchronized by complex interactions of environmental cues to ensure optimal survival and growth of individuals and their offspring. However, this synchronicity is threatened by global change, which modifies the hydrological and thermal regimes of rivers worldwide. In particular, the asynchronous evolution of river temperature and flow can alter the duration and frequency of environmental windows suitable for the migration of diadromous fish. In this research project, we first developed the ‘Choc’ method to explore temporal CHanges in the OCcurrence of associations in bivariate time series. We applied this method to several case studies, which highlighted how global change has altered the conditions under which the endangered European eel and Atlantic salmon migrate, and how they have responded to these environmental changes. Recently, reconstructed (1963-2019) and projected (2020-2100) daily river temperature and flow data have been modelled over the entire hydrographic network of the Loire catchment (France). We combined this extensive dataset with daily fish passages available at fishways to assess the spatial and seasonal variability of trends in temperature-flow associations at a large scale. We then described how it has affected and will likely affect migration conditions of Atlantic salmon, allis shad and sea lamprey in the Loire catchment. Finally, we developed indicators to quantify past, present and future environmental suitability for their migration that allow comparison between rivers and tributaries, thereby providing operational results for the conservation of diadromous species and the prioritization of management actions in the context of global change. (Anthony Maire) 05 Jul 2023
  • [hal-03738584] Distinct impacts of food restriction and warming on life history traits affect population fitness in vertebrate ectotherms

    The reduction of body size with warming has been proposed as the third universal response to global warming, besides geographical and phenological shifts. Observed body size shifts in ectotherms are mostly attributed to the temperature size rule (TSR) stating that warming speeds up initial growth rate but leads to smaller size when food availability does not limit growth. Nevertheless, climate warming can decrease food availability by modifying biochemical cycles and primary production. Food availability can also influence growth, fecundity and survival and thus potentially modulate the effect of temperature on life history strategies and fitness. However, the interactive effects of temperature and food availability on life history traits have been mostly studied in small invertebrate species where life history traits have been mainly considered in isolation. In contrast, we have limited information on (1) how temperature and food availability jointly influence life history traits in vertebrate predators and (2) how changes in different life history traits combines to influence fitness and population growth. To fill this gap, we investigated under laboratory conditions the independent and interactive effects of temperature (20 or 30 °C) and food availability (restricted or ad libitum) on the growth, fecundity and survival of the medaka fish Oryzias latipes. We next used our empirical estimates of vital rates as input parameters of an Integral Projection model (IPM) to predict how modifications in vital rates translate into generation time and population growth rate (i.e. mean fitness). Our results confirm that warming leads to a higher initial growth rate and lower size leading to crossed growth curves between the two temperatures. Food-restricted fish were smaller than ad libitum fed fish throughout the experiment, leading to nested growth curves. Fish reared at 30 °C matured younger, had smaller size at maturity, had a higher fecundity but had a shorter life span than fish reared at 20 °C. Food restriction increased survival probabilities under both temperature conditions corresponding to a "eat little die old" strategy. According to the IPM, warming reduces generation time and increases mean fitness in comparison to the cold treatments. Food restriction increased generation time and fitness in the cold treatment but had no effect in the warm treatment. Our results highlight the importance of accounting for the interaction between temperature and food availability to understand how body size shifts can affects vital rates and population demography. This is of importance in the context of global warming as resources (e.g., phytoplankton and zooplankton communities in aquatic ecosystems) are predicted to change in size structure and total abundance with increasing temperatures. Interestingly, our results suggest that food restriction has a weaker effect on fish mean fitness under warming. (Simon Bazin) 09 May 2023
  • [hal-04305582] N‐dimensional hypervolumes in trait‐based ecology: Does occupancy rate matter?

    Abstract Many methods for estimating the functional diversity of biological communities rely on measuring geometrical properties of n‐dimensional hypervolumes in a trait space. To date, these properties are calculated from individual hypervolumes or their pairwise combinations. Our capacity to detect functional diversity patterns due to the overlap of multiple hypervolumes is, thus, limited. Here, we propose a new approach for estimating functional diversity from a set of hypervolumes. We rely on the concept of occupancy rate, defined as the mean or absolute number of hypervolumes enclosing a given point in the trait space. Furthermore, we describe a permutation test to identify regions of the trait space in which the occupancy rate of two sets of hypervolumes differs. We illustrate the utility of our approach over existing methods with two examples on aquatic macroinvertebrates. The first example shows how occupancy rate relates to the stability of trait space utilisation due to increased flow intermittency and allows the identification of taxa in regions of the trait space with low occupancy rates. The second example shows how the permutation test based on occupancy rates can detect differences in trait space utilisation due to river morphology variation even with a high degree of overlap among input hypervolumes. Our newly developed approach is particularly suitable in functional diversity analysis when investigating patterns of overlap among multiple hypervolumes. We emphasise the need to consider analyses based on occupancy rate into functional diversity estimation. Read the free Plain Language Summary for this article on the Journal blog. (Alex Laini) 24 Nov 2023
  • [hal-04177227] Assessing resilience and sensitivity patterns for fish and phytoplankton in French lakes

    Ecosystem vulnerability is crucial information for conservation managers. We assessed the sensitivity and resilience (vulnerability components) patterns of fish and phytoplankton assemblages in French lakes (natural and artificial). We measured resilience (functional redundancy) and sensitivity, an index considering three characteristics of rarity for species. We hypothesized that geographically close lakes have similar resilience and sensitivity for fish assemblages (H1). Then, we tested the correlation between environmental gradients and resilience and sensitivity components, assuming that fish and phytoplankton do not respond similarly to environmental factors and that, consequently, there is no congruence between sensitivity and resilience patterns between of two groups. Also, we tested the hypotheses that species-rich assemblages show higher resilience and sensitivity in French lakes (H2); the highest values of resilience and sensitivity are related to phytoplankton (H3); and assemblages from natural lakes have higher resilience and sensitivity level (H4). We found similar resilience levels in spatially close fish assemblages due to fish dispersal limitations that contributed to create regional patterns in functional structure. Besides, acidity and eutrophication processes are good indicators of sensitivity level for fish. There is a mismatch in resilience and sensitivity levels between fish and phytoplankton, reinforcing importance of using a multi-taxa approach. Also, the components were positively related to taxonomic richness in assemblages showing importance of conserving biodiversity. Finally, we observed higher values of resilience and sensitivity for phytoplankton, as expected for a highly diverse group. Additionally, phytoplankton assemblages in natural lakes showed higher resilience levels than artificial environments, confirming the importance of preserving natural systems to conserve ecosystem functionality. (Barbbara Silva Rocha) 04 Aug 2023
  • [hal-04305541] Long-term trends in crayfish invasions across European rivers

    Europe has experienced a substantial increase in non-indigenous crayfish species (NICS) since the mid-20th century due to their extensive use in fisheries, aquaculture and, more recently, pet trade. Despite relatively long invasion histories of some NICS and negative impacts on biodiversity and ecosystem functioning, large spatio-temporal analyses of their occurrences are lacking. Here, we used a large freshwater macroinvertebrate database to evaluate what information on NICS can be obtained from widely applied biomonitoring approaches and how usable such data is for descriptions of trends in identified NICS species. We found 160 time-series containing NICS between 1983 and 2019, to infer temporal patterns and environmental drivers of species and region-specific trends. Using a combination of metaregression and generalized linear models, we found no significant temporal trend for the abundance of any species (Procambarus clarkii, Pacifastacus leniusculus or Faxonius limosus) at the European scale, but identified species-specific predictors of abundances. While analysis of the spatial range expansion of NICS was positive (i.e. increasing spread) in England and negative (significant retreat) in northern Spain, no trend was detected in Hungary and the DutchGerman-Luxembourg region. The average invasion velocity varied among countries, ranging from 30 km/year in with declines being fastest in the Dutch-German-Luxembourg region, and much slower in England. Considering that NICS pose a substantial threat to aquatic biodiversity across Europe, our study highlights the utility and importance (Ismael Soto) 24 Nov 2023
  • [hal-04302963] Clogging modulates the copper effects on microbial communities of streambed sediments

    The hyporheic zone, i.e. the water-saturated sediment beneath and alongside the riverbed, is exposed to multiple stressors. Agricultural-watershed rivers are frequently exposed to two concomitant stressors: clogging and copper contamination. However, one stressor exposure can increase sensitivity to a second stressor. The aim of this study was to experimentally test the cumulative effects of these two stressors on copper distribution and structural and functional microbial communities responses in the hyporheic zone. A slow filtration column experiment was conducted to compare the effects of 3 treatments of increasing complexity: 'Reference', 'Copper-contaminated' (dissolved copper added at 191 mu g L-1), and 'Clogging+Copper' (dissolved copper + addition of 2 cm of fine sediment). Microbial community structure and activities were studied at 4 column sediment depths. The results showed that clogging did not modify the distribution of copper, which remained fixed in the first few centimetres. In the first few centimetres, clogging had a stimulating effect on microbial activities whereas copper had limited effects mainly on leucine aminopeptidase activity and microbial community tolerance to copper. The subsurface zone thus hosts significant different microbial communities from the communities in the deeper zones that were protected from surface stressors. This experiment confirms the valuable filtering role played by the hyporheic zone and shows that microbial responses are strongly correlated to microhabitat-scale physicochemical conditions in sediment. (Laura Kergoat) 23 Nov 2023
  • [hal-04044983] Horizontal ramping rate framework to quantify hydropeaking stranding risk for fish

    Hydropeaking due to hydropower production can have negative impacts on aquatic fauna. One of the mechanisms for causing impacts on fish and aquatic macroinvertebrates is linked to the rapid dewatering of habitats, which can result in stranding or trapping. The magnitude of these impacts depends both on the characteristics of the flow variations and of the river morphology, as well as biological parameters (species, behavior, etc). When discharge is rapidly reduced, the risk of impacts on fishes (and notably the risk of fish stranding in dewatered zones along the riverbank) is frequently assessed by calculations of vertical ramping velocity among other methods. However, to assess fish stranding risks, the lateral ramping velocity calculated as a horizontal ramping rate (HRR) appears to be a more relevant indicator as it directly measures shoreline drawdown rates. HRR has the advantage of integrating river morphology, but it remains challenging to calculate HRRs in complex situations such as braided rivers. Using hydraulic simulations of the Durance, a gravel bed braided river, we have developed an innovative approach for HRR calculation. Considering two simulated flows, the algorithms for the calculations require partitioning the finite elements into wet and drying meshes. To recommend rates of lowering discharges during hydropeaking events, further studies are required to evaluate more precisely HRR limits for fish stranding regarding biotic and abiotic parameters: species, sizes, nychthemeral cycles, temperature, substrate, and so forth. (Yann Le Coarer) 24 Mar 2023
  • [hal-04028923] Robust identification of potential habitats of a rare demersal species (blackspot seabream) in the Northeast Atlantic

    Species distribution models (SDM) are commonly used to identify potential habitats. When fitting them to heterogeneous, opportunistically collated presence/absence data, imbalance in the number of presence and absence observations often occurs, which could influence results. To robustly identify potential habitats for blackspot seabream (Pagellus bogaraveo) throughout its distribution area in the Northeast Atlantic and the western Mediterranean Sea, we used an ensemble species distribution modelling (eSDM) approach, modelling gridded presence-absence data with environmental predictors for two types of occurrence data sets. The first data set displayed the observed unbalanced spatially heterogeneous presence/absence ratio and the second a balanced presence/absence ratio. The data covered the full distribution area, including the European Atlantic shelf, the Azorean region and the Western Mediterranean Sea. Across these regions, populations display variable status. The main environmental predictors for potential habitats were bathymetry and annual maximum SST. The fitted ensemble compromise (eSDM) was projected over the whole grid to create a habitat suitability map. This map exhibited higher probabilities of presence for the balanced-ratio data set. A binary presence-absence map was then generated using optimized presence probability thresholds for four validation indices. Using the true skill statistic to optimize the threshold, the surface areas of the binary presence-absence map was 53% smaller for the balanced data set than for the observed unbalanced data set. However, the choice of validation index had an even greater impact (up to 15 000%). This indicates that studies using opportunistic data for SDM fitting need to pay attention to the effects of presence/absence data imbalance and the choice of validation index to fully evaluate uncertainty. (Lola de Cubber) 14 Mar 2023
  • [hal-04305592] Species sensitivity and functional uniqueness determine the response of macroinvertebrate functional diversity to species loss in urban streams

    Abstract Land‐use change, particularly urbanisation, has led to an unprecedented decline in species and functional diversity worldwide. However, the mechanism through which such species loss affects functional diversity remains unclear. Here, we aimed to elucidate this mechanism from the perspectives of the association between species sensitivity and functional uniqueness (i.e., their relative contribution to functional diversity) and their related functional traits. We collected stream macroinvertebrates and measured environmental and land‐use variables from 152 sites in the highly urbanised Qiantang River Basin in the Zhejiang Province of eastern China. Firstly, we evaluated the sensitivity to urbanisation and functional uniqueness of each macroinvertebrate taxon to identify their association patterns. Secondly, we examined the decline in functional diversity in response to taxon loss by comparing simulated ordered and random taxon loss scenarios. Finally, we identified sensitivity‐related traits (SRT) and functional uniqueness‐related traits (URT) using the Mann–Whitney U‐test to elucidate their role in shaping functional response patterns to taxon loss. Urbanisation showed a remarkable effect on the taxonomic and functional diversity of macroinvertebrates. Functional diversity declined nonlinearly with taxon loss, with the threshold response shifting to a rapid decline after 29.7%–60.0% taxa were lost. The sensitivities of ephemeropteran, plecopteran and trichopteran taxa (EPT) were negatively associated with their functional uniqueness, although this association was not detected when considering all macroinvertebrates. We identified 11 SRT and nine URT, but only one URT overlapped SRT. The association between species sensitivity and its functional uniqueness shapes functional decline patterns in response to taxon loss. Overlap patterns of SRT and URT offer novel insights into mechanisms underlying stress‐induced decline in functional diversity. The process of functional diversity decline in response to species loss caused by urbanisation also may be affected by species turnover or even compensated for by non‐native species in real world ecosystems. How functional diversity responds to species loss remains an open topic that needs to be cautiously addressed. (Jin Gao) 24 Nov 2023
  • [hal-04001803] Identifying the impact of toxicity on stream macroinvertebrate communities in a multi-stressor context based on national ecological and ecotoxicological monitoring databases

    In situ bioassays are used to measure the harmful effects induced by mixtures of toxic chemicals in watercourses. In France, national-scale biomonitoring data are available including invertebrate surveys and in-field chemical toxicity measures with caged gammarids to assess environmental toxicity of mixtures of chemicals. The main objective of our study is to present a proof-of-concept approach identifying possible links between in-field chemical toxicity, stressors and the ecological status. We used two active biomonitoring databases comprising lethal toxicity (222 in situ measures of gammarid mortality) and sublethal toxicity (101 in situ measures of feeding inhibition). We measured the ecological status of each active biomonitoring site using the I2M2 metric (macroinvertebrate-based multimetric index), accounted for known stressors of nutrients and organic matter, hydromorphology and chemical toxicity. We observed a negative relationship between stressors (hydromorphology, nutrients and organic matter, and chemical toxicity) and the good ecological status. This relationship was aggravated in watercourses where toxicity indicators were degraded. We validated this hypothesis for instance with nutrients and organic matter like nitrates or hydromorphological conditions like percentage of vegetation on banks. Future international assesments concerning the role of in-field toxic pollution on the ecological status in a multi-stressor context are now possible via the current methodology. (Noëlle Sarkis) 23 Feb 2023
  • [hal-04044901] Modelling macroinvertebrate hydraulic preferences in alpine streams

    Alpine streams face rapid hydrological changes due to the effects of global warming, glacier melting, and increased water uses such as hydropower production. Defining environmental flows (e-flow) is crucial to mitigate the ecological impacts of flow alterations. Among e-flow assessment methods, hydraulic habitat models predict changes in habitat suitability for aquatic species under different flow scenarios. They couple hydraulic models of stream reaches with biological models relating the abundance of taxa to microhabitat hydraulics. However, there is currently no suitable biological models for alpine, often fishless streams. In this study, we develop biological models for dominant macroinvertebrate taxa in alpine streams and compare their responses to hydraulics with those published in lowland streams. Using data collected in 150 microhabitats along a gradient of shear stress within five alpine streams, we performed generalized linear mixed models relating macroinvertebrate abundance to microhabitat hydraulics (shear stress, flow velocity, Froude number and water depth). We developed biological models for 41 taxa, and observed significant microhabitat selection for shear stress (18 taxa), velocity (20), Froude number (21), and depth (11). Most of them presented consistent responses across studied alpine streams, with shear stress and velocity as the main drivers. For common taxa, shapes of macroinvertebrate responses to hydraulics were comparable with those observed in lowland streams. Nevertheless, taxa preferred slightly lower shear stress in alpine streams compared to lowland streams, probably due to high-fine sediment and oxygen concentrations, especially for taxa feeding on autochthonous organic matter. Many (23%) abundant taxa are rheophilic in alpine streams, thereby threatened by flow reduction, including the glacial stream specialists Diamesinae and Rhithrogena delphinensis, which will be also affected by glacier retreat. Combined with hydraulic models, our biological models will facilitate more robust e-flow assessments, thereby reducing the impacts of flow alterations on alpine aquatic ecosystems. (Juliette Becquet) 24 Mar 2023
  • [hal-03946704] Disentangling the components of coastal fish biodiversity in southern Brittany by applying an environmental DNA approach

    The global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Such strategies should not only focus on maximizing the number of species (i.e., taxonomic diversity) but also the diversity of phylogenetic histories and ecological functions within communities. To support future conservation decisions, multicomponent biodiversity monitoring can be combined with high-throughput species assemblage detection methods such as environmental DNA (eDNA) metabarcoding. Here, we used eDNA to assess fish biodiversity along the coast of southern Brittany (France, Iroise Sea). We filtered surface marine water from 17 sampling stations and applied an eDNA metabarcoding approach targeting Actinopterygii and Elasmobranchii taxa. We documented three complementary biodiversity components—taxonomic, phylogenetic, and functional diversity—and three diversity facets—richness, divergence and regularity. We identified a north/south contrast with higher diversity for the three facets of the biodiversity components in the northern part of the study area. The northern communities showed higher species richness, stronger phylogenetic overdispersion and lower functional clustering compared to the ones in the southern part, due to the higher diversity of habitats (reefs, rocky shores) and restricted access for fishing. Moreover, we also detected a higher level of taxonomic, phylogenetic, and functional uniqueness in many offshore stations compared to more coastal ones, with the presence of species typically living at greater depths (> 300 m), which suggests an influence of hydrodynamic structures and currents on eDNA dispersion and hence sample composition. eDNA metabarcoding can, therefore, be used as an efficient sampling method to reveal fine-scale community compositions and in combination with functional and phylogenetic information to document multicomponent biodiversity gradients in coastal marine systems. (Romane Rozanski) 19 Jan 2023
  • [hal-03946769] Contrasting Phylogeographic Patterns of Mitochondrial and Genome-Wide Variation in the Groundwater Amphipod Crangonyx islandicus That Survived the Ice Age in Iceland

    The analysis of phylogeographic patterns has often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mitonuclear discordances and complex evolutionary histories. These enigmatic scenarios, which may involve stochastic lineage sorting, ancestral hybridization, past dispersal and secondary contacts, are increasingly scrutinized with a new generation of genomic tools such as RADseq, which also poses additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing the mito-nuclear discordance of an endemic groundwater amphipod from Iceland, Crangonyx islandicus, which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture, which may have been further strengthened by natural selection. (David Eme) 19 Jan 2023
  • [hal-03946746] A multispecies, intraspecific functional traits data set on fish species from the Bay of Biscay, France

    The global biodiversity crisis due to anthropogenic pressures jeopardizes marine ecosystem functioning and services. Community responses to these environmental changes can be assessed through functional diversity, a biodiversity component related to organism–environment interactions, and estimated through biological traits related to organism functions (locomotion, feeding mode, and reproduction). Fish play a key role in marine systems functioning and supply proteins for billions of humans worldwide, yet most of the knowledge is limited to several commercial species and little is known about the intraspecific variability of their functional traits. The data provided here consist of 867 records of individuals from 85 species of ray-finned (Actinopterygii) and cartilaginous (Chondrichthyes) fish sampled in the Bay of Biscay (Atlantic, France) between autumn 2017 and 2019. We provided for each individual the taxonomic classification, 16 ecomorphological measures (5 directly made on fresh individuals and 11 realized using individual pictures) that were converted into nine ecomorphological traits classically documented in the literature (biomass, protrusion, oral gape shape, surface and position, eye size and position, body transversal shape and surface, pectoral fin position and caudal peduncle throttling) and eight life history traits obtained from FishBase (maximum length, average depth, depth range, trophic level, reproduction mode, fertilization mode, parental care, vertical position in the water column). These traits document several functions such as dispersion, feeding mode, habitat use, position in the food web, and reproduction. To improve the development of new traits, we provided a picture of each individual with an ROI file containing the different morpho-anatomical measures made using “ImageJ” software and an R function to extract them. In addition, we provided the metadata from each sampling site (years, dates, stations, sampling hours, strata, gears, latitudes, longitudes, and depths) and environmental variables measured in situ (conductivity, salinity, water temperature, water density, and air temperature). This data set accounting for the intraspecific variability among 85 fish species is of interest to better understand the effects of environmental forcing in a global change context as in the Bay of Biscay, a highly fished transition zone harboring mixed assemblages of boreal, temperate, and subtropical fish species that are susceptible to display variability in functional trait to adapt to changing conditions. The data set is freely available without copyright restrictions; users should cite this paper in research products (publications, presentations, reports, etc.) derived from the data set. (Romane Rozanski) 19 Jan 2023
  • [hal-03946736] Causes, Responses, and Implications of Anthropogenic versus Natural Flow Intermittence in River Networks

    Rivers that do not flow year-round are the predominant type of running waters on Earth. Despite a burgeoning literature on natural flow intermittence (NFI), knowledge about the hydrological causes and ecological effects of human-induced, anthropogenic flow intermittence (AFI) remains limited. NFI and AFI could generate contrasting hydrological and biological responses in rivers because of distinct underlying causes of drying and evolutionary adaptations of their biota. We first review the causes of AFI and show how different anthropogenic drivers alter the timing, frequency and duration of drying, compared with NFI. Second, we evaluate the possible differences in biodiversity responses, ecological functions, and ecosystem services between NFI and AFI. Last, we outline knowledge gaps and management needs related to AFI. Because of the distinct hydrologic characteristics and ecological impacts of AFI, ignoring the distinction between NFI and AFI could undermine management of intermittent rivers and ephemeral streams and exacerbate risks to the ecosystems and societies downstream. (T. Datry) 19 Jan 2023
  • [hal-03893760] Catchment‐scale applications of hydraulic habitat models: Climate change effects on fish

    Approaches available for estimating the ecological impacts of climate change on aquatic communities in river networks range from detailed mechanistic models applicable locally to correlative approaches applicable globally. Among them, hydraulic habitat models (HABMs) link hydraulic models of streams with biological models that reflect how organisms select microhabitat hydraulics. Coarser but more general species distribution models (SDMs) predict changes in geographic distributions; they generally involve coarse predictors such as air temperature or distance to source but neglect proximate habitat descriptors such as microhabitat hydraulics. We propose an original application of HABM for predicting the ecological impacts of climate change at large scales, a comparison of their predictions with those of SDM and a linkage of the two modelling approaches. We showcase our approach in a large catchment (Rhône River) where an available distributed hydrological model estimates present and future unregulated daily flows over the whole river network. Despite large local uncertainties, simulations showed that climate change may strongly reduce low flow percentiles (e.g., a median reduction of 38.6% for a pessimistic climate scenario), inducing important alteration of fish hydraulic habitat suitability (e.g., a median loss of 3.9%–18.7% for three modelled fish species with contrasting habitat use: brown trout, barbel and sculpin). The HABM and SDM individually predicted consistent or opposite fish responses to climate change, depending on the species and their habitat requirements. Our results illustrate that accounting for ecological responses to proximate habitat variables such as hydraulics can strongly modify projections related to climate change. (Maxime Morel) 11 Dec 2022
  • [hal-04026599] Introducing HyPeak: An international network on hydropeaking research, practice, and policy

    An increase in the demand for renewable energy is driving hydropower development and its integration with variable renewable energy sources. When hydropower is produced flexibly from hydropower plants, it causes rapid and frequent artificial flow fluctuations in rivers, a phenomenon known as hydropeaking. Hydropeaking and associated hydrological alterations cause multiple impacts on riverine habitats with cascading effects on ecosystem functioning and structure. Given the significance of hydropeaking’s ecological and socio-economic implications, mitigation requires an inter- and transdisciplinary approach. An interdisciplinary network called HyPeak has been conceived to enrich international research initiatives and support hydropower planning and policy. HyPeak has been founded based on exchange and networking activities linking scientists from several countries where hydropeaking has been widespread for decades and numerous studies dedicated to the topic have been carried out. HyPeak aims to integrate members from other countries and continents in which hydropower production plays a relevant role, and grow to be a reference group that provides expert advice on the topic to policy-makers, as well as researchers, stakeholders and practitioners in the field of hydropeaking. (Maria Alp) 13 Mar 2023
  • [hal-04058236] HSV-1 cellular model reveals links between aggresome formation and early step of Alzheimer's disease

    Many studies highlight the potential link between the chronic degenerative Alzheimer's disease and the infection by the herpes simplex virus type-1 (HSV-1). However, the molecular mechanisms making possible this HSV-1-dependent process remain to be understood. Using neuronal cells expressing the wild type form of amyloid precursor protein (APP) infected by HSV-1, we characterized a representative cellular model of the early stage of the sporadic form of the disease and unraveled a molecular mechanism sustaining this HSV-1- Alzheimer's disease interplay. Here, we show that HSV-1 induces caspase-dependent production of the 42 amino-acid long amyloid peptide (A beta 42) oligomers followed by their accumulation in neuronal cells. A beta 42 oligomers and activated caspase 3 (casp3A) concentrate into intracytoplasmic structures observed in Alzheimer's disease neuronal cells called aggresomes. This casp3A accumulation in aggresomes during HSV-1 infection limits the execution of apoptosis until its term, similarly to an abortosis-like event occurring in Alzheimer's disease neuronal cells patients. Indeed, this particular HSV-1 driven cellular context, representative of early stages of the disease, sustains a failed apoptosis mechanism that could explain the chronic amplification of A beta 42 production characteristic of Alzheimer's disease patients. Finally, we show that combination of flurbiprofen, a non-steroidal anti-inflammatory drug (NSAID), with caspase inhibitor reduced drastically HSV-1-induced A beta 42 oligomers production. This provided mechanistic insights supporting the conclusion of clinical trials showing that NSAIDs reduced Alzheimer's disease incidence in early stage of the disease. Therefore, from our study we propose that caspase-dependent production of A beta 42 oligomers together with the abortosis-like event represents a vicious circle in early Alzheimer's disease stages leading to a chronic amplification of A beta 42 oligomers that contributes to the establishment of degenerative disorder like Alzheimer's disease in patients infected by HSV-1. Interestingly this process could be targeted by an association of NSAID with caspase inhibitors. (Marie Alexandra Albaret) 20 Dec 2023
  • [insu-04071495] Deep denitrification: Stream and groundwater biogeochemistry reveal contrasted but connected worlds above and below

    Excess nutrients from agricultural and urban development have created a cascade of ecological crises around the globe. Nutrient pollution has triggered eutrophication in most freshwater and coastal ecosystems, contributing to a loss in biodiversity, harm to human health, and trillions in economic damage every year. Much of the research conducted on nutrient transport and retention has focused on surface environments, which are both easy to access and biologically active. However, surface characteristics of watersheds, such as land use and network configuration, often do not explain the variation in nutrient retention observed in rivers, lakes, and estuaries. Recent research suggests subsurface processes and characteristics may be more important than previously thought in determining watershed-level nutrient fluxes and removal. In a small watershed in western France, we used a multi-tracer approach to compare surface and subsurface nitrate dynamics at commensurate spatiotemporal scales. We combined 3-D hydrological modeling with a rich biogeochemical dataset from 20 wells and 15 stream locations. Water chemistry in the surface and subsurface showed high temporal variability, but groundwater was substantially more spatially variable, attributable to long transport times (10–60 years) and patchy distribution of the iron and sulfur electron donors fueling autotrophic denitrification. Isotopes of nitrate and sulfate revealed fundamentally different processes dominating the surface (heterotrophic denitrification and sulfate reduction) and subsurface (autotrophic denitrification and sulfate production). Agricultural land use was associated with elevated nitrate in surface water, but subsurface nitrate concentration was decoupled from land use. Dissolved silica and sulfate are affordable tracers of residence time and nitrogen removal that are relatively stable in surface and subsurface environments. Together, these findings reveal distinct but adjacent and connected biogeochemical worlds in the surface and subsurface. Characterizing how these worlds are linked and decoupled is critical to meeting water quality targets and addressing water issues in the Anthropocene. (Emilee Severe) 26 Feb 2024
  • [hal-03843377] Tracking a killer shrimp: Dikerogammarus villosus invasion dynamics across Europe

    Aim: Invasive alien species are a growing problem worldwide due to their ecological, economic and human health impacts. The "killer shrimp" Dikerogammarus villosus is a notorious invasive alien amphipod from the Ponto-Caspian region that has invaded many fresh and brackish waters across Europe. Understandings of large-scale population dynamics of highly impactful invaders such as D. villosus are lacking, inhibiting predictions of impact and efficient timing of management strategies. Hence, our aim was to assess trends and dynamics of D. villosus as well as its impacts in freshwater rivers and streams. Location: Europe. Methods: We analysed 96 European time series between 1994 and 2019 and identified trends in the relative abundance (i.e. dominance %) of D. villosus in invaded time series, as well as a set of site-specific characteristics to identify drivers and determinants of population changes and invasion dynamics using meta-regression modelling. We also looked at the spread over space and time to estimate the invasion speed (km/year) of D. villosus in Europe. We investigated the impact of D. villosus abundance on recipient community metrics (i.e. abundance, taxa richness, temporal turnover, Shannon diversity and Pielou evenness) using generalized linear models. Results: Population trends varied across the time series. Nevertheless, community dominance of D. villosus increased over time across all time series. The frequency of occurrences (used as a proxy for invader spread) was well described by a Pareto distribution, whereby we estimated a lag phase (i.e. the time between introduction and spatial expansion) of approximately 28 years, followed by a gradual increase before new occurrences declined rapidly in the long term. D. villosus population change was associated with decreased taxa richness, community turnover and Shannon diversity. Main Conclusion: Our results show that D. villosus is well-established in European waters and its abundance significantly alters ecological communities. However, the multidecadal lag phase prior to observed spatial expansion suggests that initial introductions by D. villosus are cryptic, thus signalling the need for more effective early detection methods. (Ismael Soto) 08 Nov 2022
  • [hal-03910907] Past hydraulics influence microhabitat selection by invertebrates and fish in hydropeaking rivers

    Hydropeaking hydropower plants are the main source of renewable energy, meeting sub-daily peaks in electricity demand. They induce rapid artificial flow variations, highly variable velocities, drift, and stranding risks for aquatic organisms. In hydropeaking reaches, microhabitat selection likely depends on both present and past hydraulics (flow velocity and water depth); this study aims to assess their relative impact. For this purpose, we used observations of fish abundance in 1,180 microhabitats (507 sampled by electrofishing, 673 by snorkeling) and of invertebrate abundance in 36 microhabitats (hyporheic and benthic) in a medium-sized hydropeaking river. We described past hydraulics of microhabitats over the 15 days preceding sampling, using a 2D hydrodynamic model, by identifying microhabitats dewatering (drying during >10 hr) or with high-velocity conditions (>1.3 m s(-1) during >10 hr). Invertebrates guilds (defined based on their selection of present hydraulics in rivers without hydropeaking) responded significantly to past hydraulics, with abundances 3.5-15.3 times lower in dewatering habitats. Selection for present hydraulics by invertebrates was different from that observed in rivers without hydropeaking. For more mobile fish, responses were weaker and different, with a "bank" guild selecting dewatering microhabitats and, secondarily, a "midstream" guild avoiding them. Selection of present hydraulics by fish was similar to that observed in rivers without hydropeaking. Overall, past hydraulics influenced microhabitat selection, with stronger effects on invertebrates and stronger effects of dewatering than of high past velocities. However, high past velocities force fish to move and invertebrates to experience a large range of velocity. (Clarisse Judes) 12 Sep 2023
  • [hal-04222956] Comparing field, probabilistic, and 2D numerical approaches to assess gravel mobility in a gravel-bed river

    Sediment transport is a key process that affects the morphology and ecological habitat diversity of rivers. As part of a gravel augmentation program to mitigate sediment deficit below a dam, gravel mobility in the Ain River in Eastern France was investigated by tracking of a large amount (n = 1,063) of PIT-tagged gravels in the field, conducting a probabilistic approach based on published tracer studies, and performing two-dimensional (2D) numerical modeling of flow and bedload transport. This comparative study highlights the strengths, weaknesses, and complementary aspects of the three approaches to the understanding of river gravel mobility. Thanks to recent technological improvements, PIT-tagged gravels provide an increasingly reliable and accurate representation of bedload movement in the field, although it remains limited in spatio-temporal resolution. Based on an exponential distribution, the probabilistic approach correctly reproduces the average trend in travel distances by the different classes of particles over hydrological periods, including one or several significant floods. Furthermore, the 2D numerical modeling accounts for the variability of local hydrodynamic conditions and can simulate realistic displacement distributions for the different classes of particles with high spatio-temporal resolution. Numerical modeling is a very encouraging approach, which makes our study original because it is the first time that the estimation of mean travel distances, the application of an exponential distribution, and the comparison with a hydrodynamic model are combined. A more effective modeling strategy involves incorporating a probabilistic transport model in the 2D numerical model to reproduce the observed scatter of the individual particle trajectories. (Fanny Arnaud) 29 Sep 2023
  • [hal-03924360] “It's dry, it has fewer charms!”: Do perceptions and values of intermittent rivers interact with their management?

    Intermittent rivers, which do not flow all year round, have biophysical functioning specificities which need to be considered when defining management policies, even more so in the current context of global change. However, in Europe intermittent rivers benefit from the same regulations as permanent rivers, which undoubtedly leads to their degradation. This paper aims to identify (1) how perceptions and values of intermittent rivers interact with their management and (2) determine whether the prospect of climate change leads the stakeholders to questioning their perceptions and values of intermittent rivers and the way we should manage them. Semi-structured interviews and mental mapping exercises were conducted with 28 various stakeholders (elected officials, fishers, river managers, and residents), all of whom lived along the French intermittent Albarine River. Qualitative analysis of the discourses and maps confirms strong interactions between the perceptions and values related to intermittent rivers and their management. The results highlight social devaluation of the intermittent section in terms of aesthetics, recreation, and biological values. They also point to the role of power plays between river managers and fishers, in the prioritization of management actions that favor perennial sections to the detriment of intermittent ones. These dynamics of devaluing and discarding intermittent sections or rivers from management plans are all the more alarming as there is little propensity among river stakeholders to think about the future of these intermittent rivers and their value in the context of climate change, where the prevalence of intermittent rivers is likely to increase dramatically. (Marylise Cottet) 05 Jan 2023
  • [hal-04049952] Temperature, productivity, and habitat characteristics collectively drive lake food web structure

    While many efforts have been devoted to understand variations in food web structure among terrestrial and aquatic ecosystems, the environmental factors influencing food web structure at large spatial scales remain hardly explored. Here, we compiled biodiversity inventories to infer food web structure of 67 French lakes using an allometric niche-based model and tested how environmental variables (temperature, productivity, and habitat) influence them. By applying a multivariate analysis on 20 metrics of food web topology, we found that food web structural variations are represented by two distinct complementary and independent structural descriptors. The first is related to the overall trophic diversity, whereas the second is related to the vertical structure. Interestingly, the trophic diversity descriptor was mostly explained by habitat size (26.7% of total deviance explained) and habitat complexity (20.1%) followed by productivity (dissolved organic carbon: 16.4%; nitrate: 9.1%) and thermal variations (10.7%). Regarding the vertical structure descriptor, it was mostly explained by water thermal seasonality (39.0% of total deviance explained) and habitat depth (31.9%) followed by habitat complexity (8.5%) and size (5.5%) as well as annual mean temperature (5.6%). Overall, we found that temperature, productivity, and habitat characteristics collectively shape lake food web structure. We also found that intermediate levels of productivity, high levels of temperature (mean and seasonality), as well as large habitats are associated with the largest and most complex food webs. Our findings, therefore, highlight the importance of focusing on these three components especially in the context of global change, as significant structural changes in aquatic food webs could be expected under increased temperature, pollution, and habitat alterations. (Camille Leclerc) 29 Mar 2023
  • [hal-04048110] Disturbance‐driven alteration of patch connectivity determines local biodiversity recovery within metacommunities

    Understanding the capacity of ecological systems to withstand and recover from disturbances is a major challenge for ecological research in the context of environmental changes. Past research has mostly focused on the local effects of disturbances on biodiversity recovery, while alterations of inter-patch connectivity induced by disturbances have received comparatively less attention. Here, we investigated the effect of disturbances on local biodiversity recovery within metacommunities. Our specific focus was on drying river networks, which are characterised by a high variability of patch connectivity. We found marked variations of local biodiversity recovery among sites and among groups of organisms with contrasting dispersal modes, which were explained by the amount of patch connectivity loss due to drying events. Local communities of flying organisms recovered more efficiently from drying events than organisms with strictly aquatic dispersal due to the capacity of the former group to overcome hydrological connectivity loss. As a general rule, loss of patch connectivity decreases community recovery, regardless of patch location in the river network, dispersal mode or drying spatial extent. The relationship between patch connectivity loss and community recovery we found in river networks is general and applicable to any spatial network with a high variability of patch connectivity. (Claire Jacquet) 27 Mar 2023
  • [hal-03712770] A whole-ecosystem experiment reveals flow-induced shifts in a stream community

    The growing threat of abrupt and irreversible changes to the functioning of freshwater ecosystems compels robust measures of tipping point thresholds. To determine benthic cyanobacteria regime shifts in a potable water supply system in the tropical Andes, we conducted a whole ecosystem-scale experiment in which we systematically diverted 20 to 90% of streamflow and measured ecological responses. Benthic cyanobacteria greatly increased with a 60% flow reduction and this tipping point was related to water temperature and nitrate concentration increases, both known to boost algal productivity. We supplemented our experiment with a regional survey collecting > 1450 flow-benthic algal measurements at streams varying in water abstraction levels. We confirmed the tipping point flow value, albeit at a slightly lower threshold (40-50%). A global literature review broadly confirmed our results with a mean tipping point at 58% of flow reduction. Our study provides robust in situ demonstrations of regime shift thresholds in running waters with potentially strong implications for environmental flows management. (Daniela Rosero-López) 04 Jul 2022
  • [hal-03896963] Light and hydrologic connectivity drive dissolved oxygen synchrony in stream networks

    Stream dissolved oxygen (DO) dynamics are an outcome of metabolic activity and subsequently regulate ecosystem functions such as in-stream solute and sediment reactions. The synchronization of DO signals in and across stream networks is both a cause and effect of the mode and timing of these functions, but there is limited empirical evidence for network patterns of DO synchrony. We used high frequency DO measurements at 42 sites spanning five catchments and stream orders to evaluate DO signal synchrony in response to variation in light (a driver of photosynthesis) and discharge (a control on DO signal spatial extent). We hypothesized that stream network DO synchrony arises when regional controls dominate: when light inputs are synchronous and when longitudinal hydrologic connectivity is high. By complement, we predicted that DO signal synchrony decreases as light becomes more asynchronous and stream flows decline or become discontinuous. Our results supported this hypothesis: greater DO signal synchrony arose with increasing light synchrony and flow connectivity. A model including these two controls explained 70% of variation in DO synchrony. We conclude that DO synchrony patterns within- and across-networks support the current paradigm of discharge and light control on stream metabolic activity. Finally, we propose that DO synchrony patterns are likely a useful prerequisite for scaling subdaily metabolism estimates to network and regional scales. (Jacob Diamond) 22 Feb 2024
  • [hal-03796552] Bilan des émissions de gaz à effet de serre RiverLy 2019

    Ce rapport vise à présenter brièvement et garder trace du bilan des émissions de gaz à effet de serre réalisé à RiverLy pour l’année 2019. Nous avons utilisé l’outil GES1point5 développé par le consortium Labos1point5. Il ne prend en considération que les émissions liées au déplacements professionnels (missions et véhicules de services), aux déplacements domicile-travail, et aux bâtiments. Les émissions liées aux achats et au numérique n’ont pas été quantifiées. (Céline Berni) 18 Oct 2022
  • [hal-03799448] Macroinvertebrate distribution associated with environmental variables in alpine streams

    Abstract Glaciers and ice caps are experiencing strong mass losses worldwide, challenging water availability, hydropower generation, and ecosystems. Here, we perform the first-ever glacier evolution projections based on deep learning by modelling the 21st century glacier evolution in the French Alps. By the end of the century, we predict a glacier volume loss between 75 and 88%. Deep learning captures a nonlinear response of glaciers to air temperature and precipitation, improving the representation of extreme mass balance rates compared to linear statistical and temperature-index models. Our results confirm an over-sensitivity of temperature-index models, often used by large-scale studies, to future warming. We argue that such models can be suitable for steep mountain glaciers. However, glacier projections under low-emission scenarios and the behaviour of flatter glaciers and ice caps are likely to be biased by mass balance models with linear sensitivities, introducing long-term biases in sea-level rise and water resources projections. (Juliette Becquet) 11 Dec 2022
  • [hal-03813778] Does hydrological connectivity control functional characteristics of artificial wetland communities? Evidence from the Rhône River

    The importance of artificial wetlands for the biodiversity of the Rhône River floodplain was assessed at twelve stations along two sections of the river. The relative roles of the local characteristics of the wetlands (e.g. available nutrients, dissolved oxygen, sediment quality) and of their connectivity with the main channel were considered for three different groups of organisms (benthic micr obes, benthic invertebrates and phytoplankton communities). The functional characteristics of these organisms were determined through their enzymatic activities (for microbes) and biological traits (for invertebrates and phytoplankton). The predicted major role of connections between the wetlands and the river channel was confirmed for environmental characteristics (water and sediment) and benthic invertebrates. Connectivity appeared to be less of a driver of benthic microbial communities and phytoplankton, which were partly or mainly controlled by wetland geometry (water depth, light penetration, and resulting organic matter production). We conclude that connectivity with the river channel needs to be considered jointly with the geometry of wetlands to provide functional solutions when defining management and restoration plans. (Maxine Thorel) 13 Oct 2022
  • [hal-03788090] Direct habitat descriptors improve the understanding of the organization of fish and macroinvertebrate communities across a large catchment

    In large-scale aquatic ecological studies, direct habitat descriptors (e.g. water temperature, hydraulics in river reaches) are often approximated by coarse-grain surrogates (e.g. air temperature, discharge respectively) since they are easier to measure or model. However, as biological variability can be very strong at the habitat scale, surrogate variables may have a limited ability to capture all of this variability, which may lead to a lesser understanding of the ecological processes or patterns of interest. In this study, we aimed to compare the capacity of direct habitat descriptors vs. surrogate environmental variables to explain the organization of fish and macroinvertebrate communities across the Loire catchment in France (10 5 km 2 ). For this purpose, we relied on high-resolution environmental data, extensive biological monitoring data (>1000 sampling stations) and multivariate analyses. Fish and macroinvertebrate abundance datasets were considered both separately and combined to assess the value of a cross-taxa approach. We found that fish and macroinvertebrate communities exhibited weak concordance in their organization and responded differently to the main ecological gradients. Such variations are probably due to fundamental differences in their life-history traits and mobility. Regardless of the biological group considered, direct habitat descriptors (water temperature and local hydraulic variables) consistently explained the organization of fish and macroinvertebrate communities better than surrogate descriptors (air temperature and river discharge). Furthermore, the organization of fish and macroinvertebrate communities was slightly better explained by the combination of direct or surrogate environmental variables when the two biological groups were considered together than when considered separately. Tied together, these results emphasize the importance of using a cross-taxa approach in association with high-resolution direct habitat variables to more accurately explain the organization of aquatic communities. (Coline Picard) 26 Sep 2022
  • [hal-03794966] Biodiversity response to glacier retreat: from glacier foreland to the ice ecosystem

    [...] (Sophie Cauvy‐fraunié) 03 Oct 2022
  • [hal-03795647] Macroinvertebrate hydraulic preference models: a tool for predicting and mitigating the impacts of water abstractions in mountain streams

    [...] (Juliette Becquet) 04 Oct 2022
  • [hal-03794989] In a context of increasing warming in the tropical Andes, the ecological structure of high elevation streams might lose cold adapted taxa and change to smaller populations

    [...] (Estefania Quenta‐herrera) 03 Oct 2022

Modification date : 03 January 2024 | Publication date : 26 May 2023 | Redactor : SW