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White-clawed crayfish, bullhead, and freshwater pearl mussel are different model organisms in terms of biological traits. Analysing their distribution patterns, habitat demands, and causes of decline may thus help to derive broader frameworks for conservation projects. This paper includes a wide-ranging literature review for these three threatened freshwater animals, then uses general patterns to make suggestions about broader protection measures for freshwater species. Each species has a patchy distribution, from local to broad spatial scales. However, we point out the difficulty to summarise such knowledge, because many variables were not consistently and/or accurately recorded by workers, and because the range of colonised habitats depends on the environmental heterogeneity within study areas. Causes of decline are chiefly related to human activities which modify the biological, chemical, and physical features of the aquatic environment, and can be classified into four types: physical habitat alterations, interspecific interactions, overfishing and poaching, and natural disturbance. By analysing causes of decline and possible actions, we develop seven general trends that could be adopted for a wider array of species. However, protection plans cannot be effective without actual collaborations between river managers, local inhabitants, and authorities. Finally, the re-introduction procedure itself (if needed) depends on the biology of the species under survey, and remains specific. At the same time, further fundamental research is needed to generalise relationships between population and habitat dynamics at different spatial and temporal scales.

We investigated the relationships between different environmental variables and the spatial distribution patterns of the stoneloach (Barbatula barbatula) at the stream system, the stream site, and the mesohabitat (riffle/pool) scales in south-western France. Stoneloach occurred at 240 sites (out of 554 sampling sites), chiefly close to the source, in areas at low elevation and with weak slopes. Population density at a site was primarily influenced by physical conditions. Stream width was positively related to the probability of presence of stoneloach within the stream system, but negatively related to local density. These results indicate that stoneloaches can occur in a wide range of streams, but they are less abundant in wide rivers, probably because of lower habitat heterogeneity. Slope was negatively correlated to both fish presence at the regional scale and local density, suggesting that stoneloach’s swimming performance were weak under greater erosive forces. These results suggested that the distribution of populations and the density of stoneloach were governed by the suitability of physical habitat. Multi-scale studies of factors influencing a species’ distribution allow to integrate patterns observed at different scales, and enhance our understanding of interactions between animals and their environment. The use of few pertinent variables in successful final models could reduce the effort and cost of data collection for water management applications.

We investigated differences in microhabitat preference curves for bullheads, Cottus gobio L., of different size-classes during low flow periods, and evaluated the influence of such differences on habitat use through Weighted Usable Area (WUA) predictions in relation to river flow in a piedmont stream in Southwest France. Water depth, current velocity, and substratum composition were used to calculate proportional use values for each size-class (SC), and to quantify size-specific microhabitat preferences. Bullhead used non-cohesive and coarse mineral particles (pebbles, cobbles, boulders), but there was a spatial segregation of individuals from different size classes (SC1–SC4). Smaller bullhead (SC1, total length 60 mm), the latter occurring below (or under) the largest particles, where current velocity is weakened and sand accumulates. SC1 bullhead had a more restricted range for each habitat descriptors, and were thus likely to require a more specific habitat type than other bullhead. The maximum WUA values and the related preferred discharges (0.15–0.75 m3 s–1) depended on the considered size-class. Our results suggest that ontogenetic niche shifts may play a role in the structure and dynamics of populations, by adjusting species' requirements to the spatial and temporal dynamics of environmental conditions, including abiotic and biotic conditions. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

We used general linear modelling to assess the influence of environmental variables on the spatial distribution patterns of the bullhead (Cottus gobio) at stream system, site, and micro- habitat scales in southwestern France. Bullheads occurred at 67 sites (out of 554 sampling sites), chiefly close to the source, in small and shallow streams. Population density at a site was primarily influenced by thermal conditions. Stream width was negatively related to the probability of pres- ence of bullheads within the stream system, but positively related to local density, showing that bullhead density could increase within a range of stream width, but that wider rivers were unsuitable. Slope was negatively correlated to bullhead’s occurrence and local density, and depth was negatively correlated to local density and microhabitat use, suggesting that bullhead’s shim- ming performance was weak under greater erosive forces. Therefore, the most significant results suggested that the distribution of populations and individuals was first governed by the suitability of physical and hydraulic habitat, then population dynamics at a site was mainly governed by the thermal regime. Multi-scale studies of factors influencing a species’ distribution thus allow to integrate patterns observed at different scales, and enhance our understanding of interactions between animals and their environment. Such models are essential in the exploratory phase of fundamental and applied investigations, because they help to target further research, and they should influence the measures to be taken in field surveys or conservation plans.

We examined diel patterns in fish distribution, size and relative density in a side-channel of the River Garonne before and after a late-summer spate as part of a study of the role of floodplain wetlands in fish recruitment. Increases in fish size (SL) at night were mostly unaffected by the spate, whereas an increase in fish density at night, not observed prior to the spate, was observed in some species post spate. Microhabitat use was variable at dusk and night before and after the spate, but dawn and daytime microhabitat use were less variable after the spate. Water velocity, macrophytes and ligneous debris were the most important microhabitat variables prior to the spate, but were replaced thereafter by substratum composition and bank slope. Changes in microhabitat electivities were most apparent in abundant species, with shifts in depth, substratum and water velocity preferences in 0+ gudgeon Gobio gobio and 0+ chub Leuciscus cephalus. Our results indicate that habitat suitability (or preference) curves and electivity profiles are influenced by variations in river discharge, emphasizing the importance of using multiple samplings (diel, within-season, between-season) when setting habitat criteria for river management and when assessing the role of floodplain wetlands in fish recruitment.

Spatial patterns in the combinations of biological traits of fish communities were studied in the Garonne River system (57 000 km 2 , south-west France). Fish species assemblages were recorded at 554 sampling sites, and the biological traits of species were described using a fuzzy-coding method. A co-inertia analysis of species distributions and biological traits identified some spatial patterns of species trait combinations. Fish species richness progressively increased from up- to downstream sections, and the longitudinal patterns of fish assemblages partitioned the river into clear biogeographic areas, such as the brown trout Salmo trutta (headwater streams), the grayling Thymallus thymallus, the barbel Barbus barbus and the bream Abramis brama zones (most downstream sections), which fitted with Huet's well-known zonation for western European rivers. Only a few biological traits, chiefly related to life-history attributes, significantly influenced the observed fish distributions. Fecundity, potential size, maximum age and reproductive factor increased from headwater to plain reaches. As a theoretical framework for assessing and predicting the functional organization of stream fish communities, spatial variations in species traits can be related to habitat conditions, thus providing explicit spatial schemes that may be useful to the design of both scientific studies and river management.

In the Midi-Pyrenees region (southwest France), the increasing number of gravel pits has allowed the wintering of numerous species of waterbirds such as Great Cormorants (Phalacrocorax carbo). The debate about cormorant predation on fish stock has been sufficiently strong to have resulted in reductions in cormorant numbers by control shooting. In this context, cormorants were studied during winters 1996/1997 and 1997/1998 at two gravel pit sites in the Garonne floodplain. Human disturbances and fish densities were found to be the main parameters determining the abundance of fishing cormorants. This work will help to prompt further research and the development of a management strategy for this species.

The diet of cormorants roosting at Malause on the Garonne River (South- West France) was studied by analyzing pellets collected during the winter 2001– 2002. This roost held a mean of 550 cormorants between October 2001 and March 2002, making it one of the most important winter roosts in France. The diet contained 14 fish species, including 10 cyprinids. Cyprinids were the most abundant prey, representing 90 % of individual fish. Bream Abramis brama between 100 and 150 mm in length were the most abundant food items, while large bream ( > 300 mm total length) were also consumed. The proportion of pellets containing bream increased from 26 % in October – November to 69 % in February – March. There was no significant change in the size of the bream over time. The next most abundant species was pikeperch Sander lucioperca present in 15.4 % of the pellets from December –January but only 2.6 % in February – March

The biomass and the biochemical composition of periphyton were studied during one year in three streams of Reunion Island. The results revealed that nutritional conditions for fish development were most favourable during the dry season. The nutritive value of periphyton was highest in the Marsouins and Mât streams and remained the lowest in the Roches stream. Food availability was strongly affected by high flow, particularly during the exceptional hydrological events of February 1998 (cyclonic high flows). Study of seasonal variations of morphophysiological characteristics and biochemical composition (lipids, proteins) of the grazer gobiidae Sicyopterus lagocephalus showed that inspite of unfavourable nutritional conditions caused by hydrological disturbances, fish continue their reproduction which coincides with the summer high flow period. The significant depletion of lipid reserves which express a deterioration in animal condition is influenced by flooding period. At this time of gonad development involving an additional energy investment, fish were not able to recover a stable nutritional state after the complete achievement of the reproduction cycle. Except during this period, there is a weak participation of the reproductive physiological processes in the seasonal changes of somatic composition of this fish.

2. The abundance and diversity of the fish assemblages in floodplain channels were modelled using Artificial Neural Network (ANN) analysis and nine variables: the abundance of the six dominant species, fish specific richness, overall abundance of 0+ fish and the Shannon index of diversity. Multiple regression analysis was also used to assess ANN performance. 3. Using 596 samples, correlation coefficients (r adjusted) between observed and estimated values of the nine dependent parameters were all highly significant (P < 0.01). Expected values from the tested data were significantly related to the observed values. The correlation coefficient between observed and estimated values (r) varied from 0.70 to 0.85. 4. The ANN provided a high quality prediction, despite the complex nature of the relationship between microhabitat composition and fish abundance. 5. Garson’s algorithm was used to provide the explanatory power needed in ecology when using black-box models. Parameters contained in the models (i.e. weighting) were used to determine the relative contributions of explanatory variables and thus to ascertain the structure of fish communities.

1. Discriminant factorial analysis (DFA) and artificial neural networks (ANN) were used to develop models of presence/absence for three species of small-bodied fish (minnow, Phoxinus phoxinus, gudgeon, Gobio gobio, and stone loach, Barbatula barbatula). 2. Fish and ten environmental variables were sampled using point abundance sampling by electrofishing in the Ariege River (France) at 464 sampling points. 3. Using DFA, the percentage of correct assignments, expressed as the percentage of individuals correctly classified over the total number of examined individuals, was 62.5% for stone loach, 66.6% for gudgeon and 78% for minnow. With back-propagation of ANN, the recognition performance obtained after 500 iterations was: 82.1% for stone loach, 87.7% for gudgeon and 90.1% for minnow. 4. The better predictive performance of the artificial neural networks holds promise for other situations with non-linearly related variables.

L'etude de l'abondance des petites especes de poissons comme le vairon est necessaire car ces especes jouent un role important dans la dynamique de la chaine alimentaire des rivieres a salmonides et cyprinides rheophiles. Dans cette etude, nous proposons l'utilisation des reseaux de neurones artificiels pour modeliser et predire l'abondance du vairon Phoxinus phoxinus a l'echelle du microhabitat. Les poissons ont ete echantillonnes par peche electrique selon la methode de l'echantillonnage ponctuel d'abondance. Dix variables du milieu ont ete prises en compte pour decrire l'environnement ponctuel des poissons : la distance a la berge, le pourcentage de blocs, de galets, de gravier, de sable, de vase et de marne, la profondeur et la vitesse du courant. Sur un total de 465 echantillons ponctuels d'abondance realises, nous avons etabli le modele de reseaux de neurones utilisant la procedure de validation croisee : par le processus de tirage aleatoire, nous avons isole 372 echantillons (soit 80 %) comme l'ensemble d'apprentissage et 93 echantillons restant (20 %) comme l'ensemble de test. Sur l'ensemble de test, la performance de prediction a atteint 92 %. Notre etude a montre ainsi les avantages de l'algorithme de la retropropagation de gradient du reseau de neurones pour une approche stochastique de l'ecologie des poissons non-salmonides.

Microbial denitrification is the main nitrogen removing process in freshwater ecosystems. The aim of this study was to show whether and how water warming (+ 2.5 °C) drives bacterial diversity and structuring and how bacterial diversity affects denitrification enzymatic activity in phototrophic river biofilms (PRB). We used water warming associated to the immediate thermal release of a nuclear power plant cooling circuit to produce natural PRB assemblages on glass slides while testing 2 temperatures (mean temperature of 17 °C versus 19.5 °C). PRB were sampled at 2 sampling times during PRB accretion (6 and 21 days) in both temperatures. Bacterial community composition was assessed using ARISA. Denitrifier community abundance and denitrification gene mRNA levels were estimated by q-PCR and qRT-PCR, respectively, of 5 genes encoding catalytic subunits of the denitrification key enzymes. Denitrification enzyme activity (DEA) was measured by the acetylene-block assay at 20 °C. A mean water warming of 2.5 °C was sufficient to produce contrasted total bacterial and denitrifier communities and, therefore, to affect DEA. Indirect temperature effect on DEA may have varied between sampling time, increasing by up to 10 the denitrification rate of 6-day-old PRB and decreasing by up to 5 the denitrification rate of 21-day-old PRB. The present results suggest that indirect effects of warming through changes in bacterial community composition, coupled to the strong direct effect of temperature on DEA already demonstrated in PRB, could modulate dissolved nitrogen removal by denitrification in rivers and streams.

Microhabitat use by minnow, Phoxinus phoxinus (L.), gudgeon, Gobio gobio (L.) and stone loach, Barbatulo barbatulo (L.) was studied during winter and summer reduced discharge periods in the Rivers Ariege, Nive and Gave de Pau, southwestern France. Fish samples were collected using point abundance eleetrofishing and data on eleven environmental variables was obtai­ ned simultaneously. Interspecific relationships and species-habitat relationships were determined and compared by season in the three rivers. The observed seasonal variations of interspecific and species-habitat relationships were related to substrate variables and instream cover which play an important role in the spatial distribution of the three fish species studied.

Denitrification is an ecosystem service of nitrogen load regulation along the terrestrial-freshwater-marine continuum. The present study documents the short-term temperature sensitivity of denitrification enzyme activity in phototrophic river biofilms as a typical microbial assemblage of this continuum. Denitrification measurements were performed using the acetylene inhibition method at four incubation temperatures: 1.1, 12.1, 21.2 and 30.9°C. For this range of temperature, N(2)O production could be fitted to an exponential function of incubation temperature, yielding mean (±standard error) activation energy of 1.42 (±0.24) eV and Q(10) of 7.0 (±1.4). This first quantification of denitrification enzyme activity temperature dependence in phototrophic river biofilms compares with previous studies performed in soils and sediments. This demonstrates the high temperature dependence of denitrification as compared to other community-level metabolisms such as respiration or photosynthesis. This result suggests that global warming can unbalance natural community metabolisms in phototrophic river biofilms and affect their biogeochemical budget.

International audience; We assessed the benefit of 11 gravel pits for the settlement of waterbird communities in an urbanized area lacking natural wetlands. Gravel pits captured 57% of the regional species pool of aquatic birds. We identified 39 species, among which five were regionally rare. We used the Self Organizing Map algorithm to calculate the probabilities of presence of species, and to bring out habitat conditions that predict assemblage patterns. The age of the pits did not correlate with assemblage composition and species richness. There was a positive influence of macrophyte cover on waterbird species richness. Larger pits did not support more species, but species richness increased with connectivity. As alternative wetland habitats, gravel pits are attractive to waterbirds, when they act as stepping stones that ensure connectivity between larger natural and/or artificial wetlands separated in space.

Our ability to demonstrate statistical patterns of invasion by non-native species will determine the success of future management projects. We investigated the suitability of self-organizing maps (SOM, neural network) for patterning habitat invasion by exotic fish species at the regional scale (Southwest France), using a binary dataset of species occurrences. The SOM visualization can be used as an analytical tool to bring out relationships between sample locations and biological variables, but in addition the weight of each species in the output of the SOM can be interpreted as its occurrence probability in various geographic areas. After training the SOM with fish presence/absence data, the k-means algorithm helped to derive three major clusters of sites (headwater, montane, and plain areas). Each cluster was divided into two subsets of sites according to non-native fish, because assemblage compositions delineated different geological areas: Pyrenees Mountains, Massif Central Mountains, and alluvial plain. Occurrence probabilities of species within our study stream system were roughly influenced by river typology, with a higher occurrence probability for most species (i.e. a greater risk) in downstream sections. Conversely, headwater streams at the highest elevations in the study area showed the lowest risk of invasion. Efficient analytical tools such as SOM may thus help to yield explicit schemes that could influence the measures to be taken in the latter phase of conservation plans.

We assessed the influence of environmental variables (elevation, stream order, distance from source, catchment area, slope, stream width, and fish species richness) on the co-occurrence patterns of the minnow, the stone loach, and the gudgeon at the stream system scale. A total of 474 sites were classified according to the seven variables using the Self-Organizing Map (neural network), and three clusters were detected (k-means algorithm). The frequency of the various fish co-occurrence patterns was calculated for each cluster, and general linear modeling was used to specify the conditions that predict the occurrence of each species. Piedmont streams were more likely to support coexisting gudgeon and minnow populations because of higher probabilities of occurrence for both species. The higher co-occurrence frequency for the three species together in headwater streams resulted from lower occurrence frequencies in gudgeon and minnow. Focusing on areas that favor the co-occurrence of species may enhance the effectiveness of conservation projects.

Most of our current understanding of rarity has come from studies of terrestrial plants and animals, whereas freshwater habitats remain poorly documented under this topic. Here we considered the spatial distribution patterns of rarity at the river catchment scale, for five freshwater taxa (fish, Ephemeroptera, Plecoptera, Trichoptera and Coleoptera) in southwestern France. The data were collected at 554 and 155 sampling sites for fish and aquatic insects, respectively. General Linear Modelling was used to assess the influence of some typological variables (elevation, stream order, distance from source, and reach slope) on local numbers of rare species (restricted range). The relative numbers of rare species per taxa varied from 16% (Plecoptera) to 59% (Trichoptera). GLM chiefly yielded highly significant correlations between rarity and distance from the source and/or elevation for all taxa, showing that numbers of rare stream species increase towards downstream areas within the stream system. The spatial patterns in rarity for the different study taxa were rather concordant, probably as a result of similar responses to environmental conditions. By focusing on integrative variables, we emphasized the influence of river typology on the rarity of aquatic animals. Areas which carry rare species may concentrate an important fraction of the regional biodiversity. If end-users need geographic models (i.e. maps) to design river management frameworks, numerical patterning is needed to provide theoretical backgrounds: by predicting what the rarity should be like in a given area, we can provide explicit spatial schemes that may be useful to target further research, and to implement management options.

The aim of this study was to investigate the influence of 5 typological variables on the spatial dis- tribution patterns of fish species richness in south-western France, and, subsequently, to analyse differ- ences in the number of species occurring in 6 major hydroregions located within the overall study area. The data were collected at 329 sampling sites. General Linear Modelling was used to assess the influ- ence of each typological variable on local fish species richness, and to determine the differences in local fish species richness between the 6 hydroregions. Local species richness was significantly influenced by altitude, slope and catchment area, whereas distance from the source and stream width showed no significant relations with local richness. The Côteaux de Gascogne hydroregion had a significantly lower species richness, whereas no significant differences occurred among other neighbouring hydroregions. These results were congruent with the spatial distribution patterns of freshwater invertebrate species richness in the area, which were analysed in previous studies. At such a regional scale, we suggest that congruent patterns between fish and invertebrate species richness are almost certainly a result of simi- lar responses by different taxa to environmental conditions, rather than to biotic interactions.

Ce travail a consisté à prédire la richesse spécifique locale de poissons dans le bassin de la Garonne à partir de trois variables environnementales : la distance à la source, l'altitude et la surface du bassin versant. Le plus souvent, la richesse spécifique d'un bassin est étudiée en utilisant des modèles de régression linéaire simple ou multiple. Dans notre travail, un réseau de neurones a été utilisé pour développer un modèle prédictif de la richesse spécifique. Deux bases de données indépendantes ont été utilisées, une pour construire et tester le modèle, l'autre pour le valider. Les coefficients de corrélation obtenus pour le test et la validation sont élevés et hautement significatifs (respectivement, r = 0,904, p est inférieur à 0,001 et r = 0,822, p est inférieur à 0,001). Près de 70% de la variation de la richesse est expliquée par les trois variables environnementales. A travers ces résultats, les réseaux de neurones artificiels peuvent être considérés comme un puissant outil prédictif face aux approches de modélisations plus traditionnelles. (Résumé d'auteur)

Riverine ecosystems are subject to a large variety of man-made influences, and in recent years a new public awareness of the need to protect rivers has emerged within the industrialized world. The present study focuses on the effect of abatement of pollution from one factory on the recovery of fish and macroinvertebrate species richness in the River Petite Baise over a 20-year period (1973-1993). Until 1973, the Petite Baise (75 km in length) received not only factory waste (nitrogenous rich effluents) but also the untreated sewage of many villages and agricultural runoff from the river's catchment. In 1970, macroinvertebrates and fishes were absent in the river despite having initially been classified as of the barbel Barbus barbus zone, and extensive efforts were made by the factory to reduce pollution to allow the riverine community to recover. Regular surveys between 1973 and 1993 revealed a progressive improvement in water quality and the recolonization of the river by macrobenthic and fish populations. Macrobenthic fauna species richness gradually increased from zero in 1970 to level 8 or 9 in 1993 (Verneaux and Tuffery method), reflecting improvements in river water quality. Fish were not observed until 40 km downstream of the factory in 1978, 16 km in 1980, and approximately 5 km by 1990. Fish species richness increased from five in 1978 (barbel, chub Leuciscus cephalus, stone loach Barbatula barbatula, minnow Phoxinus phoxinus, gudgeon Gobio gobio) to eight in 1990 (the carnivorous brown trout Salmo fario, the omnivorous chub, and six benthophagous fishes: gudgeon, barbel, minnow, stone loach, sofie Chondrostoma toxostoma, carp Cyprinus carpio). Fish biomass 45 km downstream the factory increased from 1 g/m2 in 1978 to more than 5 g/m2 by 1990. Recolonization of the river, in particular those areas furthest downstream from the factory, occurred as a result of reductions in the nitrogen inputs emanating from the factory.

As with many rivers of the Pyrenees Mountains, reservoirs on the River Ariege (SW Francc) are used for hydroelectricity generation, irrigation and to maintain summer flows in the River Garonne. Two river reservoirs on the River Ariege were simultaneously emptied in April 1991 to remove accumulated sediment. Fish and ten environmental variables were sampled using Point Abundance Sampling by electrofishing before (February 1991) and one year later (February 1992) at three study sites downstream of the dams. We examined the short-term impact of reservoir cleaning on the relative abundance, habitat availability and habitat use of three species of small fish: minnow Phoxinus phoxinus (L.), gudgeon Gobio gobio (L.) and stone loach Barbatula barbatula (L.).¶After the reservoir cleaning, areas covered by gravel, sand and mud increased significantly as the result of the sediment release. The three species did not react in the same manner to these environmental changes. Stone loach appeared to be the most sensitive species, with its relative abundance decreasing at all sites. Conversely, minnow seemed to be the most resistant species and as such is a leading pioneer species for colonizing new or impacted stretches of rivers channels. Finally, the number of gudgeon decreased particularly at the most downstream site where large deposits of mud were recorded.

Relationships between environmental variables and 0+fish in the upper River Garonne (France) were studied at different habitat scales during late August 1995. In total, 3911 0+ fish representing 21 species were sampled using point abundance sampling by electrofishing. Fish reproductive function of floodplain channels was evaluated using principal components analysis of 0+ fish distributions (in absence/presence), with distinction of the three main channel types (flowing, partially abandoned and abandoned channels). A descriptive model of microhabitat use and microhabitat profiles of 0+ fish was developed for the more frequently encountered species using canonical correspondence analysis and an electivity index combined with chi-square analysis. Water velocity, water depth and distance from the bank were the most important microhabitat variables, followed by bank gradient and bottom composition. Partially-abandoned channels provide conditions particularly suitable to 0+ fish, with submerged vegetation in these side-channels serving many of the fishes as refuge and feeding areas. Similarities in microhabitat use were found with respect to 0+ juvenile fish in the Danube flood plain (Slovakia/Hungary), the upper River Rhone (France) and the River Great Ouse catchment (England).