No abstract

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Climate and land-use change drive a suite of stressors that shape ecosystems and interact to yield complex ecological responses, i.e. additive, antagonistic and synergistic effects.Currently we know little about the spatial scale relevant for the outcome of such interactions and about effect sizes. This knowledge gap needs to be filled to underpin future land management decisions or climate mitigation interventions, for protecting and restoring freshwater ecosystems. The study combines data across scales from 33 mesocosm experiments with those from 14 river basins and 22 cross-basin studies in Europe producing 174 combinations of paired-stressor effects on a biological response variable. Generalised linear models showed that only one of the two stressors had a significant effect in 39% of the analysed cases, 28% of the paired-stressor combinations resulted in additive and 33% in interactive (antagonistic, synergistic, opposing or reversal) effects. For lakes the frequency of additive and interactive effects was similar for all spatial scales addressed, while for rivers this frequency increased with scale. Nutrient enrichment was the overriding stressor for lakes, generally exceeding those of secondary stressors. For rivers, the effects of nutrient enrichment were dependent on the specific stressor combination and biological response variable. These results vindicate the traditional focus of lake restoration and management on nutrient stress, while highlighting that river management requires more bespoke management solutions.

We analysed the sensitivity of European Trichoptera (caddisfly) species to climate change impacts based on their distribution and ecological preferences, and compared the fraction of species potentially endangered by climate change between the European ecoregions. The study covers 23 European ecoregions as defined by Illies (1978). For 1134 Trichoptera species and subspecies, we coded 29 parameters describing biological and ecological preferences and distribution based on the evaluation of more than 1400 literature references. Five parameters served to describe the species sensitivity to climate change impacts: endemism, preference for springs, preference for cold water temperatures, short emergence period, and restricted ecological niches in terms of feeding types. Of the European Trichoptera species and subspecies, 47.9 % are endemic, 23.1 % have a strong preference for springs, 21.9 % are cold stenothermic, 35.5 % have a short emergence period, and 43.7 % are feeding type specialists. The fraction of endemic species meeting at least one of the four other sensitivity criteria mentioned above is highest in the Iberic-Macaronesian Region (30.2 % of all species), about 20 % in several other south European ecoregions, and about 10 % in high mountain ranges. In 15 out of 23 ecoregions (including all northern European and lowland ecoregions) the proportion is less than 3 %. The high fraction of potentially endangered species in southern Europe is a result of speciation during the Pleistocene. Species having colonised northern Europe afterwards have generally a large geographical range and are mainly generalists and thus buffered against climate change impacts.

The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh-and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a

We examined the phylogenetic relationships between species and genera within the caddisfly subfamily Drusinae (Trichoptera: Limnephilidae) using sequence data from two mitochondrial loci (cytochrome oxidase 1, large subunit rRNA) and one nuclear gene (wingless). Sequence data were analysed for 28 species from five genera from the subfamily. We analysed individual and combined data sets using a Bayesian Markov Chain Monte Carlo and a maximum parsimony approach and compared the performance of each partition for resolving phylogenetic relationships at this level. In terms of resolution and phylogenetic utility wingless outperformed the two mitochondrial gene partitions. Using both Shimodaira-Hasegawa and expected likelihood weights tests we tested several hypotheses of relationships previously inferred based on adult morphological characters. The data did not support the generic concept, or many previously proposed species groupings, based on adult morphology. In contrast, the molecular data correlated with the morphology and feeding ecology of larvae. Using Bayesian ancestral character state reconstructions we inferred the evolution of feeding ecology and relevant larval morphological characters. Our analyses showed that within the subfamily Drusinae two derived feeding types evolved. One of these--grazing epilithic algae--is otherwise unusual in the Limnephilidae and may have promoted the high degree of diversity in the Drusinae.

The paper provides a synoptic key to the genera of final instar European Trichoptera larvae. The most important characters are illustrated by colour photos, with arrows highlighting the diagnostic features. A short descriptive text gives additional information for each decision and guides the reader through the determination process.

100Effective identification of species using short DNA fragments (DNA barcoding and DNA 101 metabarcoding) requires reliable sequence reference libraries of known taxa. Both 102 taxonomically comprehensive coverage and content quality are important for sufficient 103 accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are 104 particularly important if molecular identification tools are to be implemented in biomonitoring 105 and reports in the context of the EU Water Framework Directive (WFD) and the Marine 106Strategy Framework Directive (MSFD). We analysed gaps in the two most important 107 reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a 108 focus on the taxa most frequently used in WFD and MSFD. Our analyses show that 109 coverage varies strongly among taxonomic groups, and among geographic regions. In 110 general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, 111 caddisflies and vascular plants) are well represented in the barcode libraries, while others 112 have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also 113 found that species monitored in several countries often are represented by barcodes in 114 reference libraries, while species monitored in a single country frequently lack sequence 115 records. A large proportion of species (up to 50%) in several taxonomic groups are only 116represented by private data in BOLD. Our results have implications for the future strategy to 117 fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the 118 monitoring of European aquatic biota under the WFD and MSFD. For example, missing 119 species relevant to monitoring in multiple countries should be prioritized. We also discuss 120 why a strategy for quality control and quality assurance of barcode reference libraries is 121 needed and recommend future steps to ensure full utilization of metabarcoding in aquatic 122 biomonitoring. 123 124