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Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2‐COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2‐COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity. [ABSTRACT FROM AUTHOR]

In Europe, large rivers have been greatly impacted by engineering and hydraulic works. The Upper Rhine channelization has notably led to a disconnection between the main channel and its floodplain and side channels. Between 1998 and 2006, unprecedented restoration projects led to the reconnection of nine Rhine side channels to the main channel or the Rhine Drainage Canal. The structures of recolonizing macroinvertebrate communities observed in the restored side channels, either in 2009 or 2010, were compared to the ones of three reference side channels. The aims of the study were (i) to analyze the recolonizing macroinvertebrate communities and (ii) to identify the drivers of the community structure. The restored side channels exhibited macroinvertebrate community structures similar to those of the reference side channels. These communities were characterized by a high abundance of nonnative and invasive taxa and a structure not linked to either the time since restoration or the water and sediment chemistry. Significant correlations existed between the macroinvertebrate community structures and the mosaics of habitats, driven by the variations in side channel morphometry and discharge. Therefore, the diversity of habitat characteristics of the side channels might help conserve and increase macroinvertebrate biodiversity at the floodplain scale. [ABSTRACT FROM AUTHOR]

The degradation of aquatic ecosystems, induced by worldwide intensification in the use of both land and aquatic resources, has highlighted the critical need for innovative methods allowing an objective quantification and ranking of anthropogenic pressure effects on aquatic organisms. Such diagnostic tools have a great potential for defining robust management responses to anthropogenic pressures. Our objective was to explore how the outputs of three diagnostic tools (based on benthic diatoms, macroinvertebrates and fishes) could be combined to (i) disentangle the temporal effects of multiple pressures over two decades and (ii) provide policy-relevant information for stream managers and decision makers. The diagnostic tools estimated, using taxonomy- and trait-based metrics, the impairment probabilities of biotic assemblages over time by different pressure categories, describing the alteration of water quality, hydromorphology and land use related to anthropogenic activities, in French streams (number of sites = 312). The main result shows that a large proportion of the time series exhibited no significant temporal patterns over the two decades (61.5% to 87.8%, depending on the used tests). Among time series exhibiting significant change, positive trends in impairment probabilities (i.e., degradation) were less frequent than negative ones, indicating a modest improvement in water quality at national scale over the study period. However, trends can be substantially different according to hydroecoregion and pressure category. The three biological compartments displayed convergent temporal responses according to the pressure category and regional context (e.g., lowland plains vs. mountains, pristine vs. agricultural regions). Altogether, this study proposes a unifying approach to integrate a vast amount of information in a single ecological diagnosis using an unparalleled database on natural and anthropized environments. Strengthening the synthesis of biological information provided by various biological compartments should be a priority before implementing evidence-based sustainable conservation and restoration actions., Competing Interests: Declaration of competing interest The achievement of this manuscript has not been influenced by competing financial, personal, or professional interests., (Copyright © 2020 Elsevier B.V. All rights reserved.)