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.

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

Lakes are common features of alpine landscapes, and the attention given to alpine lakes has increased recently in response to increased recognition of the important role that these freshwaters play as sensible indicators of climate change. Despite this general research interest, there is nevertheless a general lack of information about zoobenthos especially of lakes in the Alps, and only few published data are available, which has made it nearly impossible to draw general conclusions in respect to benthic community structure, profundal and/or littoral food webs. This paper aims to explore the relationships between main environmental/catchment properties of 55 lakes and their littoral benthic fauna across three regions of the Alps. We provide updated information on relative abundance, species richness, distribution and ecology of macroinvertebrates which occur and are typical in the littoral of high-mountain lakes of the Alps. These lakes were located in the Lago-Maggiore Watershed (Italy and Switzerland), in South Tyrol (Italy) and in North/East Tyrol (Austria), between 1840 and 2796 m a.s.l., in catchments undisturbed by human activities. As the studied lakes are situated above the tree line, they were characterised by low nutrient levels indicating an oligotrophic status. Lake water chemistry corresponded closely to the geo-lithology of the catchment and some parameters (especially nutrient concentrations) differed between the regions. The macroinvertebrates were dominated by insects which to a high degree were chironomid larvae and pupae. Other insect orders were typical cold stenotherm species of Ephemeroptera, Plecoptera and Trichoptera. Non-insect macroinvertebrates contributed to the 144 taxa found. Other than lake size and catchment area, the faunal parameters exhibited a clearer pattern along altitude. Macroinvertebrates per sample increased with higher elevation, reached their maximum in lakes between 2400 and 2600 m a.s.l., but decreased strongly above 2600 m. The altitudinal pattern of species richness and Shannon diversity resembled each other being highest between 2001 and 2200 m a.s.l., but decreased when going lower and higher, respectively.Various patterns and trends along altitude were also evident when individual groups were analysed within the individual sampling regions. The somewhat conflicting trends of various biocoenotic indices let assume that factors other than altitude are also responsible for the structure of faunal assemblages in the littoral of alpine lakes. Six variables (were selected by the CCA analysis where these three groups of lakes were identified: (1) lakes with a higher alkalinity (higher pH, conductivity, ion concentration), a higher relative vegetation cover (compared to the ''bare rocks'' on the opposite side) and lower nitrate levels; (2) lakes with a higher portion of ''bare rocks'' in their catchments and higher nitrate levels; and (3) a smaller group of lakes with higher ammonia levels and a boggy environment. Geographical patterns seemed to have weak effects on the...

The chironomid fauna living in running waters in the Southern Alps was investigated from an ecological and biogeographical point of view: 202 species were identified (not including terrestrial species). It must be emphasised that species identification is tentative within some genera, especially those awaiting revision (e.g., Boreoheptagyia, Chaetocladius). Although much taxonomic work was done in the past on the chironomid Alpine fauna, there are still many unsolved problems. Most of the species found are widespread in the Palearctic Region, with no evidence of bio-geographical barriers separating different Alpine sectors. Really a relatively high number of species reported from the northern and western side (France, Switzerland, Austria) of the Alps was not captured on the southern side (Italy), whereas most species found on the southern side are also present on the northern one. Very few species are reported from southern side only. Lack of sampling, imperfect taxonomic knowledge and different environmental conditions between the northern and southern sides may be responsible of this result. A comparison of the fauna of the southern Alps with the fauna of the Apennines suggests that the differences are probably more related to ecological conditions (lack of glaciers in the Apennines) than to biogeographical barriers. Different chironomid assemblages colonise manifold habitat types: strict cold-stenothermal species tolerating high current velocity (e.g., Diamesa latitarsis -steinboecki group) are almost the sole inhabitants of kryal biotopes, while other cold-stenothermal species are restricted to cold springs (Diamesa dampfi, D. incallida, Tokunagaia rectangularis, T. tonollii), there are also species characteristic of hygropetric habitats (Syndiamesa edwardsi, S. nigra) or restricted to lacustrine habitats (Corynoneura lacustris, Paratanytarsus austriacus). It must be emphasised that different responses to environmental factors can be observed between species belonging to the same genus (e.g., Diamesa, Eukiefferiella, Orthocladius, Paratrichocladius), so species identification is really needed for a good ecological work. Water temperature, current velocity, substrate type are the most critical factors, sometime chironomid species appear to be rather opportunistic and their presence or absence cannot be clearly related to a well defined range of values of environmental variables: be it a lack of knowledge or a real datum will be the task of future studies. The waters of the Alps are still relatively unpolluted, but hydraulic stress due to river damming and canalization is a serious problem for macrofauna conservation, and as the glaciers retreat, the species confined to the glacial snouts are at risk of extinction, some of them possibly even before their existence be discovered.w The complete database with detailed taxonomical, ecological and biogeographical information can be obtained by the senior author to request (e-mail: bruno.rossaro@unimi.it). A table with species response to environmental variables is ...

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