Small Shallow Lakes and ponds (SSLs) provide numerous ecosystem services and harbour unique biodiversity. They are very vulnerable to human disturbances and play a central role in ecosystem functioning. In this study, we aimed to disentangle the role of environmental variables in the composition and richness of invertebrate communities using datasets collected from 143 French SSLs with minimal impact from human activities. The SSLs were sampled across four climatic ecoregions, encompassing various geologies and elevations. A hierarchical classification revealed a clear separation into two groups: (1) highland waterbodies and (2) lowland waterbodies. The main environmental variables identified by the db-RDA were elevation associated with climate, and the presence of fish, along with interrelated variables such as SSLs morphology. Generalised additive models GAMs that combined diversity and composition indices or taxonomic richness with determinant environmental variables demonstrated that (1) elevation, mesohabitat complexity and the presence of exotic crayfish strongly influenced the structure, richness, and composition of macroinvertebrate communities, and (2) the presence of fish had a significant impact only on community composition (e.g., reducing the relative richness of typical pond-swimmer taxa). Furthermore, even though connectivity with other waterbodies influenced the macroinvertebrate communities, its impact appeared to be less significant than elevation, climate, and local variables such as the presence of predators (fish or crayfish).

Small shallow lakes and ponds (SSWs) have high conservation value and support numerous ecosystem services. However, these small ecosystems face many threats, including eutrophication and internal biotic pressures like Cyprinidae or exotic bioturbators crayfish, which tend to shift biodiverse SSWs to a turbid state dominated by phytoplankton unfitted to numerous usages, and compromise the effectiveness of their restoration. The ecological quality of SSWs and the efficiency of their management still remain poorly evaluated because of the lack of adapted tools. To fill this gap, we propose a new multimetric index (BECOME) and a diagnostic tool (BECOMEd) both based on macrophyte and invertebrate communities. BECOME exhibits a high sensitivity to the impact of surrounding crops, urbanization and fertilized meadows, morphological alterations, and various internal biotic sources of alterations, in a wide variety of geological and climatic contexts. BECOME is especially innovative, because taking into account internal biotic sources of pressures neglected by most of the existing biological WFD-compliant indices for European lakes and ponds, despite their importance in SSW threats. BECOMEd allows to identify the major alteration sources and estimates their relative contribution to SSW degradation, helping managers to prioritize actions or to evaluate their effectiveness. The statistical design applied for the index construction has been fitted to develop biological index for ecosystems influenced by a wide amplitude of numerous environmental conditions. This design could be easily applied elsewhere in the world, for SSWs but also for other types of ecosystems.

Small shallow lakes (SSLs) have great conservation value and support numerous ecosystem services. However, these small ecosystems are faced with many threats, including eutrophication, which tends to shift biodiverse SSLs to a turbid state dominated by phytoplankton. The ecological quality of SSLs still remains poorly evaluated because of the lack of adapted tools. We propose a new trophic index—TIM2S—based on the tolerance range of 245 macrophyte species to total phosphorus. As a single trophic index can favour oligotrophic ecosystems and their associated species to the detriment of more eutrophic but rare species, we converted TIM2S into a predictive reference-based model. Then, we compared TIM2S with five existing trophic indices in their efficiency to discriminate trophic levels and disentangle eight anthropogenic or internal pressures. TIM2S was the only index strongly correlated with total phosphorus and able to discriminate trophic levels. Most existing trophic indices are expert-based, and reflect community alteration rather than eutrophication. These expert-based indices are also dependent on numerous environmental factors, highlighting the need for robust predictive models to evaluate ecological statuses accurately. TIM2S is Water Framework Directive-compatible and can be used widely in Europe to evaluate the trophic status and trophic alterations of SSLs.

Les corridors rivulaires sont les habitats les plus diversifiés et complexes du globe, sièges de nombreux processus indispensables au maintien de la qualité de l’eau et de la biodiversité. Les Diptères, second plus vaste groupe d’espèces d’insectes dans le monde, possèdent des exigences écologiques susceptibles d’exprimer la complexité des habitats rivulaires et des échanges hydriques de subsurface. De plus, il s’agit du groupe le plus abondant et le plus diversifié de nos corridors rivulaires. Ils occupent donc un rôle majeur dans les réseaux trophiques des cours d’eau et des écosystèmes terrestres riverains. Une méthode rapide d’échantillonnage des imagos de Diptères rivulaires ou aquatiques a été appliquée sur onze stations dont cinq du Massif central, tandis que la qualité de leur corridor rivulaire a été caractérisée à partir de l’indice IBCR. Les relations entre communautés de Diptères et caractéristiques du corridor rivulaire ont été analysées. Pour cela, une approche taxonomique traditionnelle et une approche fonctionnelle basée sur les traits bio-écologiques de leurs larves (alimentation et affinité à l’eau) ont été utilisées. 252 taxons de Diptères, dont sept espèces citées pour la première fois en France ont été identifiés. Le climat, l’état de conservation et la diversité des écoulements des cours d’eau du Puy-de-Dôme semblent particulièrement favorables aux communautés de Diptères rivulaires. Nos résultats indiquent qu’un corridor rivulaire plus ancien, plus large et disposant d’une dynamique fluviale favorisant une mosaïque complexe d’habitats accueille une plus grande diversité d’espèces et de modes alimentaires et d’affinités à l’eau des larves. De plus, l’échantillonnage des Diptères donne des indications sur la capacité d’accueil des habitats hygropétriques et intertidaux, permettant de mieux valoriser les travaux de restauration hydromorphologique.

Small shallow lakes (SSL) are reservoirs of biodiversity and provide numerous ecosystem services. Therefore, tools to easily and rapidly assess the biological integrity and conservation value of these aquatic ecosystems have been increasingly requested by environmental managers. In this study, we propose a new sampling method for monitoring aquatic invertebrates. This method, called S3i, allows to sample SSL with a surface area from 1 m2 to at least 20 ha. We applied the method to 268 SSL in France and used generalised additive models to investigate factors that correlate with (1) total richness, and (2) richness and relative abundance of functional group ε, i.e. group of taxa exclusive of SSL richness and determining SSL functioning. Elevation, surface area, and distance from the source—a proxy of river and watershed connectivity—were identified as determinants of invertebrate richness. Invasive crayfish may directly impact total and ε-richness, whereas fish impact ε-richness and ε-abundances. Shoreline vegetation and vegetation cover were especially determinant for total richness, ε-richness, and ε-relative abundance. The S3i was successfully applied to a wide diversity of SSL in France. The sampling method can be considered as rapid, reproductible, and representative for monitoring aquatic invertebrates in SSL and should be applied to the management of a worldwide range of small shallow lakes.

Macrophytes play an important role in the functioning and structuring of aquatic environments but rapid mass development of invasive macrophytes is causing global concerns. Macroinvertebrate richness and abundance are strongly influenced by macrophytes as macrophytes offer habitats and food resources, increase structural heterogeneity, and provide refuges. Meanwhile, the presence of macrophytes affects the efficiency of standard sampling methods for macroinvertebrates. These effects are not well studied but are leading to biased management decisions. To fill in this knowledge gap, we analysed macroinvertebrate communities from four lakes in four countries in Europe and Africa with mass development of invasive macrophytes. We compared macroinvertebrate communities in sediment samples from a plant-free part of the lake with those in sediment and sweep samples taken within macrophyte stands. We showed that taxa richness and density were higher in sediment samples beneath invasive macrophyte stands compared to plant-free habitats. Unique taxa were found in each sample type. Sampling efficiency of each sampling method varies greatly across lakes especially when replication is low. The taxonomic richness of macroinvertebrates within invasive macrophyte stands is often underestimated compared to open water sections with the same number of samples. To reach a high sampling coverage, a higher number of samples is necessary for sampling within invasive macrophytes. Our findings call for the development of a method that allows for comparable sampling within and outside of macrophyte stands. Such method will be the foundation for future research and management of aquatic systems.

Macrophytes are key to the functioning of small shallow lakes (SSLs) because they maintain a clear water state through numerous positive feedbacks. The composition of macrophyte communities changes under anthropogenic pressures; as a result, tools designed to easily and rapidly assess their structure and composition are increasingly requested. We tested three sampling methods (the S3m sampling method, a stratified method, and a mapped inventory) to monitor macrophytes in 26 SSLs. The effect of each method was evaluated on seven descriptors of macrophyte communities, including the median conservation value. The results were comparable for the three methods, but the stratified method failed to accurately monitor the median conservation value and the number of species present at a low frequency, including exotic and patrimonial species, hence serious consequences for management decisions. S3m was applied to 262 SSLs ranging from 1 m2 to 43 ha in surface area. Generalised additive models were used to investigate the environmental factors correlated with four conservation value or ecosystem functioning descriptors. The S3m method showed that surface area, distance from the source, elevation, and bank verticality were determinants of macrophyte richness. Invasive crayfish impacted the macrophyte richness and the coverage of submerged macrophytes, whereas fish presence increased the macrophyte richness and the percentage of exotic macrophytes and reduced patrimonial interest. S3m was successfully applied to a wide diversity of SSLs in France. It proved to be rapid, reproducible, and representative for monitoring macrophytes in SSLs. Therefore, it should be applied for SSL management.

Small shallow lakes (SSL) support exceptionally high and original biodiversity, providing numerous ecosystem services. Their small size makes them especially sensitive to anthropic activities, which cause a shift to dysfunctional turbid states and induce loss of services and biodiversity. In this study we investigated the relationships between environmental factors and macrophyte communities. Macrophytes play a crucial role in maintaining functional clear states. Better understanding the factors determining the composition and richness of aquatic plant communities in least-impacted conditions may be useful to protect these shallow lakes. We inventoried macrophyte communities and collected chemical, climatic, and morphological data from 89 least-impacted SSL widely distributed in France. SSL were sampled across four climatic ecoregions, various geologies, and elevations. Hierarchical cluster analysis showed a clear separation of four macrophyte assemblages strongly associated with mineralization. Determinant factors identified by distance-based redundancy analysis (db-RDA) analysis were, in order of importance, geology, distance from source (DIS, a proxy for connectivity with river hydrosystems), surface area, climate, and hydroperiod (water permanency). Surprisingly, at a country-wide scale, climate and hydroperiod filter macrophyte composition weakly. Geology and DIS are the major determinants of community composition, whereas surface area determines floristic richness. DIS was identified as a determinant in freshwater lentic ecosystems for the first time.

Biomonitoring is central to the European Union's Water Framework Directive (WFD) and to the French water and aquatic environmental law, but most diatom indices do not separate different anthropogenic impacts. To address this gap, the effect of water chemistry on diatom ecological guilds and life forms was assessed in order to indicate stream perturbations. Generalised additive models (GAMs) were built on a large-scale data set of 1571 samples from the French monitoring network. The relationships between diatom ecological guild and life form metrics were investigated by Principal components analysis and the results predicted by GAMs. The models characterised eight chemical parameters that modified adaptive strategies (ecological guilds) and growth morphology (life forms). Total phosphorus, conductivity, nitrate and pH are the main influencing factors, followed by temperature, dissolved oxygen and organic matter. The findings confirm three groups of diatoms with different adaptive strategies: 1 – fast moving species, 2 – species growing close to the substrate and 3 – species extending to the surface layers of the biofilm. Thirteen diatom metrics displayed a variety of responses to different ranges of the eight chemical parameters. These metrics could be used to help to identify and quantify which chemical alterations are caused by polluted effluents in rivers.

Shallow lakes and ponds are valuable ecosystems for conservation management. Aquatic invertebrates constitute a large proportion of diversity in these ecosystems, but their assessment is potentially time consuming and requires great expertise. The use of indicator taxa to estimate invertebrate diversity may resolve part of these difficulties. These indicators are rarely identified or. their reliability is uncertain, i.e. they are based on partial inventories, neglecting groups with high diversity. In this study, invertebrate richness was assessed from 46 sites in France in various altitudinal, climatic, geological, human-impacted, and hydro-morphological contexts. Invertebrate identification was performed as accurately as possible in all taxonomic groups. Several potential indicators of diversity based on five key criteria were tested: strong direct correlation, identification facilities, strong cross-taxon congruence, low complementarity of the sampled habitats, and ubiquity for selected indicators. Three approaches were proposed to define these indicator groups: (1) a single taxonomic group as indicator, (2) a combination of targeted groups, and (3) a holistic inventory at low taxonomic resolution as a classical rapid assessment method for freshwater ecosystems. Results show that it is not recommended to use only one indicator group. The choice of several targeted groups could be a good intermediate solution but is not without bias. The rapid assessment inventory proposed is the most valuable method, and allows the estimation of invertebrate richness with a quasi-perfect correlation.

Chemical and biological assessments of waterbodies are required to fulfil the objectives of the European Water Framework Directive (EU Off J 327:1–72, 2000 ). Many past studies have been focused on water chemistry uncertainties, but few have been carried out on the hydrobiological aspects. Considerable research on macroinvertebrates has highlighted the mosaic habitat impact on the macroinvertebrate distribution, substrate type and within-substrate heterogeneity as uncertainty sources. We thus studied the effect of substrate variability on the metrics of two French biological indices (normalized index IBGN and new index I2M2 metrics) using experimental field sampling based on substrate replicates. For each of the nine substrates studied, a minimum of 2 sites were selected (among a total of 31 sites) in 7 hydroecoregions (HER). Ten replicates per substrate and site were collected where possible. We obtained 315 faunistic lists associated with 315 substrate replicates. Twelve metrics, such as the Shannon index and variety class, were calculated by list. We used multidimensional scaling and similarity indices to analyse the substrate variability effect. Our results highlighted the extent of HER and site features on the within-substrate heterogeneity. Faunistic lists and metrics varied more in root and sand substrates than in other substrates. I2M2 metrics, i.e. ASPT, taxonomic richness or H’, calculated on each replicate, eliminated the intrasubstrate variability.

The European Water Framework Directive has required chemical and biological assessments in waterbodies. While studies of water chemistry uncertainties have existed for a long time, few studies have been carried out in hydrobiology. Our aim was to study the role of uncertainties defined as any action that may cause a data error on the French index “Indice Biologique des Macrophytes de Rivières” IBMR based on the macrophyte compartment. IBMR gives the trophic status of the river. The selected uncertainties were based on the surveyor effect both in situ and in laboratory, such as taxa omission, species identification error and cover class error. We proposed an innovative approach close to sensitivity analysis using controlled virtual changes in taxa identification and cover classes based on two confusion matrices. The creation of new experimental floristic lists and the calculation of metrics according to random specified errors allowed us to measure the effect of these errors on the IBMR and the trophic status. The taxa identification errors and combined errors (taxa identification and cover class) always had a stronger impact than cover class errors. To limit their impact, surveyor training, confrontation between surveyors and a quality control approach could be applied.

In Europe, the number of establishment of non-native species, especially from Ponto-Caspian area, has dramatically increased over the past decades and induced important changes in macroinvertebrate assemblages, mainly in large rivers. However, although many Ponto-Caspian species were established in adjacent countries, only two Ponto-Caspian amphipods were formally observed in French hydrosystems since 1996. To update our knowledge on the present distribution of the Ponto-Caspian species in France, we collected amphipods from 203 sites in the Rhine, Meuse and Seine River basins in 2008 and again in 2009. Thirteen amphipod species were found in the study area. Among them, four were first formally recorded in France (Dikerogammarus haemobaphes, Dikerogammarus bispinosus, Echinogammarus ischnus, and Echinogammarus trichiatus). Our study revealed three different corridors used by these species to arrive in France. We also observed a different pattern of colonization for each species, which might indicate some between-species differences in their preferences for environmental conditions. The snapshot of the early distributions of these recently established species may hence be used to study the invasion pattern in France in order to manage their potential impact in and outside France.