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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.

Flow cytometry (FCM) offers a multiparametric technology capable of characterizing single extracellular vesicles (EVs). However, most flow cytometers are designed to detect cells, which are larger than EVs. Whereas cells exceed the background noise, signals originating from EVs partly overlap with the background noise, thereby making EVs more difficult to detect than cells. This technical mismatch together with complexity of EV‐containing fluids causes limitations and challenges with conducting, interpreting and reproducing EV FCM experiments. To address and overcome these challenges, researchers from the International Society for Extracellular Vesicles (ISEV), International Society for Advancement of Cytometry (ISAC), and the International Society on Thrombosis and Haemostasis (ISTH) joined forces and initiated the EV FCM working group. To improve the interpretation, reporting, and reproducibility of future EV FCM data, the EV FCM working group published an ISEV position manuscript outlining a framework of minimum information that should be reported about an FCM experiment on single EVs (MIFlowCyt‐EV). However, the framework contains limited background information. Therefore, the goal of this compendium is to provide the background information necessary to design and conduct reproducible EV FCM experiments. This compendium contains background information on EVs, the interaction between light and EVs, FCM hardware, experimental design and preanalytical procedures, sample preparation, assay controls, instrument data acquisition and calibration, EV characterization, and data reporting. Although this compendium focuses on EVs, many concepts and explanations could also be applied to FCM detection of other particles within the EV size range, such as bacteria, lipoprotein particles, milk fat globules, and viruses.

Distribution maps of cetaceans and seabirds at basin and monthly scales are needed for conservation and marine management. These are usually created from standardised and systematic aerial and vessel surveys, with recorded animal densities interpolated across study areas. However, distribution maps at basin and monthly scales have previously not been possible because individual surveys have restricted spatial and temporal coverage.This study develops an alternative approach consisting of: (1) collating diverse survey data to maximise spatial and temporal coverage, (2) using detection functions to estimate variation in the surface area covered (km2) among these surveys, standardising measurements of effort and animal densities, and (3) developing species distribution models (SDM) that overcome issues with heterogeneous and uneven coverage.2.68 million km of survey data in the North‐East Atlantic between 1980 and 2018 were collated and standardised. SDM using Generalized Linear Models and General Estimating Equations in a hurdle approach were developed. Distribution maps were then created for 12 cetacean and 12 seabird species at 10 km and monthly resolution. Qualitative and quantitative assessment indicated good model performance.Synthesis and applications. This study provides the largest ever collation and standardisation of diverse survey data for cetaceans and seabirds, and the most comprehensive distribution maps of these taxa in the North‐East Atlantic. These distribution maps have numerous applications including the identification of important areas needing protection, and the quantification of overlap between vulnerable species and anthropogenic activities. This study demonstrates how the analysis of existing and diverse survey data can meet conservation and marine management needs.

The management and mitigation of chemical pollution are key elements of sustainable development initiatives that aim to provide safe and clean water. While environmental scientists are developing the capabilities to assess the fate, (eco)toxicity and risks of a plethora of synthetic chemicals comprehensively, notorious pollution scenarios and decontamination challenges call for targeted and case-specific evaluation of chemical hazards. Here we review the utility and perspectives of compound-specific isotope analysis for obtaining an understanding of environmental processes that allows one to identify pollution sources, assess contaminant (bio)transformation and gain insights into reaction pathways. Using three prototypical scenarios of water contamination, namely point-source pollution of groundwater at contaminated sites, diffuse pollution of soils and surface waters through pesticide use and the abatement of pharmaceuticals and disinfection by-products in water treatment systems, we illustrate both success stories of compound-specific isotope analysis and current developments to address challenges for future applications.Using three prototypical scenarios of water contamination from legacy pollutants at contaminated sites, agricultural use of pesticides and abatement of pharmaceuticals and disinfection by-products in water treatment systems, this Review illustrates success stories of compound-specific isotope analyses and ongoing developments for future applications.

Intermittent rivers and ephemeral streams (IRES) – waterways in which flow ceases periodically or that dry completely – are found worldwide, and their frequency and extent are expected to increase in the future in response to global climate change and growing anthropogenic demand for fresh water. Repeated wet–dry cycles generate highly dynamic settings within river networks composed of aquatic and terrestrial habitats, which act as evolutionary triggers for aquatic and terrestrial biota. Drying also alters functions and processes within river networks, with consequences for ecosystem services. Despite the emergence of promising conceptual and methodological developments, our understanding of the occurrence and diversity of organisms in these ecosystems is limited primarily due to their coupled aquatic–terrestrial characteristics. Novel genomic tools based on high-throughput sequencing have the potential to tackle unanswered questions of pivotal importance to predict future change in IRES. Here, we outline why genomic tools are needed to assess these dynamic ecosystems from the population to the metacommunity scale, and their potential role in bridging ecological–evolutionary dynamics.

Characterizing the diversity of demographic strategies among species can inform research in topics such as trait syndromes, community stability, coexistence, and ecological succession. However, this diversity can depend on the spatial scale considered: at the landscape scale, species often form metapopulations, that is sets of local, sometimes short-lived, populations, inhabiting discrete habitat patches. Metapopulation dynamics are most frequently analyzed in individual species or pairs of interacting species because of the large amount of data required for multiple species, and because species vary in their perceptions of what constitutes a favorable or unfavorable habitat. Here we evaluate, using a case study, whether a metapopulation model can be used to generate accurate estimates of demographic parameters and to describe the diversity of dynamics, responses to environment, and prospects of long-term persistence in a guild of species inhabiting a common fragmented landscape. We applied this approach to a guild of 22 mollusk species that inhabit freshwater habitats on two islands of Guadeloupe, to compare metapopulation dynamics among species. We analyzed a 15-year time series of occupancy records for 278 sites using a multistate occupancy model that estimated colonization and extinction rates as a function of site-specific and year-specific environmental covariates, then used model results to simulate future island metapopulation dynamics. Despite the diverse array of metapopulation trajectories—a mix of species with either stable, increasing, declining, or fluctuating metapopulations—and the inherent challenges associated with such data (e.g., imperfect detection, spatial and temporal heterogeneity), our model accurately captured among-patch variation in suitability for many mollusk taxa. The dynamics of rare species or species with habitat preferences not fully captured by the retained set of covariates were less well described. For several species, we detected a negative correlation between extinction and colonization. This variation in habitat suitability created species-specific extinction-resistant pockets in the landscape. Our comparative analysis also revealed that species had distinct strategies for metapopulation dynamics, such as “fast-turnover” species with both a high proportion of occupied sites and a high rate of site extinction in the landscape.

The exceptional diversity of freshwater fauna of the Mediterranean Basin currently faces a crisis in which climate change combined with overexploitation of freshwaters heavily threatens the local fauna. In this context, it is urgent to define conservation priorities on how to best protect freshwater biodiversity. One of the main limits to define such actions remains the lack of knowledge in many countries. In this study, we test the usefulness of molecular data (COI gene) combined with morphological identification to better predict the pattern of biological diversity and threats of climate change on freshwater biodiversity. We focused our study on the freshwater amphipods as model organisms in order to define conservation strategies in Tunisia, one of the most threatened countries. Our results confirmed that amphipods diversity is largely underestimated with nine species identified by their morphology and 33–39 species assigned depending on delimited with the most parsimonious molecular delimitation method. The distribution of amphipods is mainly restricted to the northern part of Tunisia and seems to be positively correlated with precipitation and negatively correlated with thermal amplitudes and precipitation fluctuations. These environmental factors are sensitive to climate change and confirm that conservation strategies need to be redefined and adjusted in the face of future climate predictions. Moreover, the total diversity and spatial distribution patterns provided by molecular methods seem to be more detailed and accurate than results based on morphology alone and nicely complement traditional species assignment.

Pitfall traps are frequently used to capture ground‐dwelling arthropods, particularly beetles, ants and spiders. The efficiency of a pitfall trapping system strongly depends on the number opening size traps, how distributed over sampling area (spatial arrangement) movement characteristics arthropods. We use numerical simulations for single species analyse trap count patterns that emerge from these variables. Arthropod individuals is modelled as correlated random walks, with multiple placed an area, catches simulated individual interaction traps. consider four different types spatial arrangements across homogeneous landscape: grid (i.e. rectangular array), transect, nested‐cross randomised. contextualise our results by considering locomotion Pterostichus melanarius , highly active carabid beetle often serving biocontrol agent suppression pest insects weeds. By simulating randomly moving we show there optimal inter‐trap separation distance (trap spacing) maximises captures, can be expressed using exact formulae in terms sizes, number. Moreover, arrangements, larger spacing maximise coverage whole suboptimal. Also, find large hierarchical order relation efficiency: grid, randomised, followed nested‐cross. However, smaller areas, this changed rate at which counts accumulate varies arrangements—eventually saturating levels. In effects, maximised narrow diffusive range does not depend type arrangement—indicating approximate mode arthropod activity, i.e. spread. Our approach simultaneously considers several important experimental design aspects providing basis optimise adapt protocols other better reflect their various purposes, such monitoring, conservation or management.

Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.

Inland navigation in Europe is proposed to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this would impact biodiversity at large scales and interact with existing stressors. Here we addressed this knowledge gap by analysing fish and macroinvertebrate community time series across large European rivers comprising 19,592 observations from 4,049 sampling sites spanning the past 32 years. We found ship traffic to be associated with biodiversity declines, that is, loss of fish and macroinvertebrate taxonomic richness, diversity and trait richness. Ship traffic was also associated with increases in taxonomic evenness, which, in concert with richness decreases, was attributed to losses in rare taxa. Ship traffic was especially harmful for benthic taxa and those preferring slow flows. These effects often depended on local land use and riparian degradation. In fish, negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was evident only when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian habitats and landscape characteristics could help to mitigate these impacts. An analysis of fish and macroinvertebrate communities in European rivers over 32 years shows that inland ship traffic is associated with declining taxonomic richness, diversity and trait richness and with increased taxonomic evenness.