The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches.

Most of the present EU Water Framework Directive (WFD) compliant fish-based assessment methods of European rivers are multi-metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitivity of the indices. In recent years, environmental (e)DNA metabarcoding techniques have progressed sufficiently to allow applications in various ecological domains as well as eDNA-based ecological assessment methods. A review of the 25 current WFD-compliant methods for river fish shows that 81% of the metrics used in these methods are expressed in richness or relative abundance and thus compatible with eDNA samples. However, more than half of the member states' methods include at least one metric related to age or size structure and would have to adapt their current fish index if reliant solely on eDNA-derived information. Most trait-based metrics expressed in richness are higher when computed from eDNA than when computed from TEF samples. Comparable values are obtained only when the TEF sampling effort increases. Depending on the species trait considered, most trait-based metrics expressed in relative abundance are significantly higher for eDNA than for TEF samples or vice versa due to over-estimation of sub-surface species or under-estimation of benthic and rare species by TEF sampling, respectively. An existing predictive fish index, adapted to make it compatible with eDNA data, delivers an ecological assessment comparable with the current approved method for 22 of the 25 sites tested. Its associated uncertainty is lower than that of current fish indices. Recommendations for the development of future fish eDNA-based indices and the associated eDNA water sampling strategy are discussed.

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

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

Typology of historical sources and the reconstruction of long-term historical changes of riverine fish: a case study of the Austrian Danube and northern Russian rivers.

Historical data are widely used in river ecology to define reference conditions or to investigate the evolution of aquatic systems. Most studies rely on printed documents from the 19th century, thus missing pre-industrial states and human impacts. This article discusses historical sources that can be used to reconstruct the development of riverine fish communities from the Late Middle Ages until the mid-20th century. Based on the studies of the Austrian Danube and northern Russian rivers, we propose a classification scheme of printed and archival sources and describe their fish ecological contents. Five types of sources were identified using the origin of sources as the first criterion: (i) early scientific surveys, (ii) fishery sources, (iii) fish trading sources, (iv) fish consumption sources and (v) cultural representations of fish. Except for early scientific surveys, all these sources were produced within economic and administrative contexts. They did not aim to report about historical fish communities, but do contain information about commercial fish and their exploitation. All historical data need further analysis for a fish ecological interpretation. Three case studies from the investigated Austrian and Russian rivers demonstrate the use of different source types and underline the necessity for a combination of different sources and a methodology combining different disciplinary approaches. Using a large variety of historical sources to reconstruct the development of past fish ecological conditions can support future river management by going beyond the usual approach of static historical reference conditions.

Predicting downstream transport distance of fish eDNA in lotic environments.

Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.

eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities.

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.

European river typologies fail to capture diatom, fish, and macrophyte community composition.

Typology systems are frequently used in applied and fundamental ecology and are relevant for environmental monitoring and conservation. They aggregate ecosystems into discrete types based on biotic and abiotic variables, assuming that ecosystems of the same type are more alike than ecosystems of different types with regard to a specific property of interest. We evaluated whether this assumption is met by the Broad River Types (BRT), a recently proposed European river typology system, that classifies river segments based on abiotic variables, when it is used to group biological communities. We compiled data on the community composition of diatoms, fishes, and aquatic macrophytes throughout Europe and evaluated whether the composition is more similar in site groups with the same river type than in site groups of different river types using analysis of similarities, classification strength, typical species analysis, and the area under zeta diversity decline curves. We compared the performance of the BRT with those of four region-based typology systems, namely, Illies Freshwater Ecoregions, the Biogeographic Regions, the Freshwater Ecoregions of the World, and the Environmental Zones, as well as spatial autocorrelation (SA) classifications. All typology systems received low scores from most evaluation methods, relative to predefined thresholds and the SA classifications. The BRT often scored lowest of all typology systems. Within each typology system, community composition overlapped considerably between site groups defined by the types of the systems. The overlap tended to be the lowest for fishes and between Illies Freshwater Ecoregions. In conclusion, we found that existing broad-scale river typology systems fail to delineate site groups with distinct and compositionally homogeneous communities of diatoms, fishes, and macrophytes. A way to improve the fit between typology systems and biological communities might be to combine segment-based and region-based typology systems to simultaneously account for local environmental variation and historical distribution patterns, thus potentially improving the utility of broad-scale typology systems for freshwater biota.

iPODfish - A new method to infer the historical occurrence of diadromous fish species along river networks.

Available information on diadromous fish species historical occurrences is generally biased and incomplete across species distribution range and spatial scales. This work aims to establish a new methodological framework (iPODfish - Inferring Past Occurrences of Diadromous Fish) to obtain a more complete representation of the historical occurrences of diadromous fish species over their full distribution range. The iPODfish is based on assumptions, rules and thresholds derived from the interplay between freshwater network features, diadromous fish species ecology and known historical occurrence. These are used to establish historical pseudo-occurrences at the segment scale, i.e., locations where the species was most likely to be present or absent. The methodology is expressed by a tree-like representation of a stepwise, information supported, decision process. It has five steps (separating main river segments from tributary segments; accounting for segments specificities; imposing the relative distance threshold; imposing the Strahler value threshold, and; establishing the sub-basin Strahler threshold), divides into two moments of application (main river followed by the tributaries) and establishes presences, pseudo-presences and pseudo-absences. The iPODfish can deal with multiple information sources, cope with data bias and provide a reliable consistent historical occurrence output at the segment scale for the known historical geographical range of the species. Despite its inference nature, iPODfish is still a conservative procedure leading to ecologically coherent outputs that may be applied to any diadromous fish species (with a relevant amount of historical data available) in any river network throughout the globe because the concepts and definitions used are general ecological features of diadromous and freshwater networks. The method outputs are applicable in biogeographical and/or macroecological studies using historical data and may prove useful to the management and conservation of diadromous fish species.

Damn those damn dams: Fluvial longitudinal connectivity impairment for European diadromous fish throughout the 20th century.

River longitudinal connectivity is crucial for diadromous fish species to reproduce and grow, its fragmentation by large dams may prevent these species to complete their life cycle. This work aims to evaluate the impact of large dams on the structural longitudinal connectivity at the European scale, from a Diadromous fish species perspective, since the beginning of the 20th century until the early 21st century. Based on large dam locations and completion year, a multitude of river impairment metrics were calculated at three spatial scales for six European oceanic regions and 12 time periods. The number of basins affected by large dams is overall low (0.4%), but for large river basins, that cover 78% of Europe's area, 69.5% of all basins, 55.4% of the sub-basins and 68.4% of river length are impaired. River network connectivity impairment became increasingly significant during the second half of the 20th century and is nowadays spatially widespread across Europe. Except for the North Atlantic, all oceanic regions have over 50% of impacted river length. Considering large river basins, the Mediterranean (95.2%) and West Atlantic (84.6%) regions are the most affected, while the Black (92.1%) and Caspian (96.0%) regions stand out as those with most compromised river length. In 60 years, Europe has gone from reduced impairment to over two-thirds of its large rivers with structural connectivity problems due to large dams. The number of such barriers increased significantly in the second half of the 20th century, especially main stem dams with decreasing distance to the river mouth. Currently, the structural longitudinal connectivity of European river networks is severely impacted. This concerns all regions considered, and those in southern Europe will face even higher challenges, given that this will be a future hot spot for hydropower development and predictably more affected by climate change.

Poly-aromatic hydrocarbon (PAH) inputs from the Rhône River to the Mediterranean Sea in relation with the hydrological cycle: impact of floods.

The concentrations of dissolved and particulate polycyclic aromatic hydrocarbons (PAHs) were monitored in waters of the Rhône River (France) every fortnight for a full calendar year, from June 1994 to May 1995. All flood events occurring over the course of the experiment were sampled at higher frequency to better quantify the impact of these extreme hydrological episodes on the annual export of PAHs to the Mediterranean Sea. This time-series indicates that more than 90% of the annual load of particulate PAHs is transported during flood episodes, with 77% discharged during the course of only one extreme flood event occurring in November 1994. During these intense events, riverine particles are depleted in PAHs while at low river discharge particles are PAH-enriched. Dissolved PAHs were less variable and less abundant than adsorbed PAHs, consistently with the low solubility of these compounds.

Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation.

Despite the ecological and societal importance of large rivers, fish sampling remains costly and limited to specific habitats (e.g., river banks). Using an eDNA metabarcoding approach, we regularly sampled 500 km of a large river (Rhône River). Comparisons with long-term electrofishing surveys demonstrated the ability of eDNA metabarcoding to qualitatively and quantitatively reveal fish assemblage structures (relative species abundance) but eDNA integrated a larger space than the classical sampling location. Combination of a literature review and field data showed that eDNA behaves in the water column like fine particulate organic matter. Its detection distance varied from a few km in a small stream to more than 100 km in a large river. To our knowledge, our results are the first demonstration of the capacity of eDNA metabarcoding to describe longitudinal fish assemblage patterns in a large river, and metabarcoding appears to be a reliable, cost-effective method for future monitoring.

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive.

Assessment of ecological status for the European Water Framework Directive (WFD) is based on "Biological Quality Elements" (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data.

The impact of two large floods (1993-1994) on sediment deposition in the Rhône delta: Implications for sustainable management.

In October 1993 and January 1994, two large floods with peak discharge of 9800 and 10,980m3/s and total suspended solid transport of 10.7×106 and 9.7×106 tons, respectively, occurred on the Rhône River. Both floods led to multiple levee breeches in the Northern part of the delta resulting in the introduction of 131×106 and 54.9×106m3 of river water, respectively. In both cases, the flood water drained to the southern lagoons and was partly pumped directly back to the Rhône or to the sea. Most of the 390,000 tons of sediment introduced remained in the Northern inundated area with accretion ranging from 70mm near the breaches to 4mm 6-8km away. This last value is close to the mean accretion value (3.7mm) inferred from the water budget and the estimation of the total quantity of sediment introduced in the flooded area. In a small area near the mouth of the Rhône river still receiving natural overflow from the river, total deposition during both floods was as high as 10cm. The Rhône delta is facing an uncertain future with projected sea-level rise. The results of this study show that large introductions of river water can help sustain the delta in the face of climate change. Controlled introductions of river water using riverside closable structures, as in being done in other deltas, could be done in a way that delivers water and sediments to the places where it is needed most and at the same time protect important infrastructure.

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.

In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.

Long-term evolution of fish communities in European mountainous rivers: past log driving effects, river management and species introduction (Salzach River, Danube).

Using historical sources from the turn of the 19th to the 20th century, we investigated the long-term evolution of the fish community in a mountainous river network and the influence of different human uses and management measures. Within the alpine Salzach catchment, historical presence was reconstructed for 26 fish species, abundance classes for 19 species. Due to channelization, flood protection and dam erections, the spatial distribution of fish species was reduced during the 20th century. Many rheophilic and eurytopic fish species historically inhabited river reaches along a wide longitudinal profile and were present in more upstream river reaches than nowadays. The decrease of species diversity in the headwater sections is a consequence of lost lateral connectivity. Strongest effects are reported for sensitive species requiring different habitat types during their life cycles (especially pike, nase, Danube salmon). One of the most important shifts from the historical fish community to the present one reflects the deliberate introduction of fish species for fisheries. Rainbow trout and brook trout, absent from the historical fish assemblage, today represent up to 29 % of the total number of fish occurrences. In contrast, log driving, one of the most common historical pressures in European mountainous rivers, did not show significant negative effects on the past fish ecological situation. This result strongly differs from the impacts of log driving and deforestation demonstrated for recent times, and could be related to the change in log driving practices during the 20th century and to the high societal value of fish before the industrialization period along with other historical pressures affecting fish in rivers without log driving. In general, our results can be valid for a large number of European mountainous rivers. They highlight the usefulness of such detailed historical studies for our understanding of the long-term evolution of fish communities and their present functioning, and point the way for future river management strategies to restore fish biodiversity.

Historical ecology of riverine fish in Europe.

The temporal dynamic of riverine ecosystems and their fish communities and populations has been addressed in ecological theory and management for several decades. A growing number of case studies on the historic development especially of European and North American rivers have been published. Nonetheless, a theoretical debate about the contributions and limits of historical approaches and interdisciplinary co-operation is lacking. This article presents a brief overview of the role of history in river and fish ecology and suggests historical ecology as a scientific field that can offer a framework for future research. Based on case studies compiled in this special issue on the "Historical ecology of riverine fish in Europe", we draw conclusions on long-term changes of fish communities, on fisheries, aquatic ecosystem management and past habitat alterations and the potential of archaeological remains and written sources to study them. We discuss how modelling of historical fish data can help elucidate the effects of climate change and human influences on rivers and fish. Finally, we account for the necessity to consider appropriate spatial and temporal scales. In conclusion we call for future comparative studies on continental and global scales and methodological development, which can benefit especially from recent advances in marine historical ecology. We suggest that future interdisciplinary studies of ecologists, hydrologists, historians and archaeologists can reveal the history of riverine ecosystems as socio-ecological systems, addressing both their natural dynamics and human dimension. Such an endeavor can also support developing management plans for habitat restoration and conservation against the background of global change.

Historical change in fish species distribution: shifting reference conditions and global warming effects.

Species distributions models (SDM) that rely on estimated relationships between present environmental conditions and species presence-absence are widely used to forecast changes of species distributions caused by global warming but far less to reconstruct historical assemblages. By compiling historical fish data from the turn to the middle of the twentieth century in a similar way for several European catchments (Rhône, Danube), and using already published SDMs based on current observations, we: (1) tested the predictive accuracy of such models for past climatic conditions, (2) compared observed and expected cumulated historical species occurrences at sub-catchment level, and (3) compared the annual variability in the predictions within one sub-catchment (Salzach) under a future climate scenario to the long-term variability of occurrences reconstructed during an extended historical period (1800-2000). We finally discuss the potential of these SDMs to define a "reference condition", the possibility of a shift in baseline condition in relation with anthropogenic pressures, and past and future climate variability. The results of this study clearly highlight the potential of SDM to reconstruct the past composition of European fish assemblages and to analyze the historical ecological status of European rivers. Assessing the uncertainty associated with species distribution projections is of primary importance before evaluating and comparing the past and future distribution of species within a given catchment.

The European Water Framework Directive at the age of 10: a critical review of the achievements with recommendations for the future.

The European Water Framework Directive (WFD), which was adopted in 2000, changed water management in all member states of the European Union fundamentally, putting aquatic ecology at the base of management decisions. Here we review the successes and problems encountered with implementation of the WFD over the past 10years and provide recommendations to further improve the implementation process. We particularly address three fields: (i) the development of assessment methods (including reference conditions, typologies and intercalibration); (ii) the implementation of assessment systems in monitoring programmes; and (iii) the consequences for river basin management plans (such as the design, monitoring and success of restoration measures). The development of assessment methods has been a transparent process and has resulted in improved and more standardised tools for assessing water bodies across Europe. The process has been more time consuming, and methods are more complex, than originally expected. Future challenges still remain, including the estimation of uncertainty of assessment results and a revision of rules in combining the results obtained with different Biological Quality Elements. A huge amount of monitoring data is now being generated for WFD purposes. Monitoring data are not centrally stored and thus poorly accessible for purposes beyond the WFD. Future challenges include enhanced data accessibility and the establishment of a Europe-wide central monitoring network of reference sites. The WFD river basin management plans base management decisions on the response of aquatic organisms to environmental stress. In contrast to the effects of degradation, the biotic response to restoration is less well-known and poorly predictable. The timescale of the WFD (obtaining good ecological status in all surface waters by 2027) is over-ambitious. Future challenges include long-term monitoring of restoration measures to understand the requirements for ecosystems to recover and prioritisation of measures according to re-colonisation potential.

Effects of natural and anthropogenic environmental changes on riverine fish assemblages: a framework for ecological assessment of rivers

A água dos rios constituem um recurso básico para a humanidade. Instrumentos biológicos eficaces (com fundamento ecológico, eficientes, rápidos e aplicáveis à regiões ecologicamente diferentes) são necessários para medir a "saúde" destes. Adaptar tais instrumentos a uma grande área geográfica requer uma compreensão detalhada dos padrões da composição da assembléia de organismos e da sua distribuição dentro e entre os corpos da água em condições naturais, e da natureza dos principais gradientes ambientais que causam ou explicam estes padrões. Uma revisão da literatura disponível pode ajudar a identificar os fatores ambientais mais consistentes que estruturam a assembléia de peixes de ambientes lóticos em condições naturais.