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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

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

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In a Quercetum petraeae-cerris forest in northeastern Hungary, we examined effects of litter input alterations on the quantity and quality soil carbon stocks and soil CO 2 emissions. Treatments at the Síkfőkút DIRT (Detritus Input and Removal Treatments) experimental site include adding (by doubling) of either leaf litter (DL) or wood (DW) (including branches, twigs, bark), and removing all aboveground litter (NL), all root inputs by trenching (NR), or removing all litter inputs (NI). Within 4 years we saw a significant decrease in soil carbon (C) concentrations in the upper 15 cm for root exclusion plots. Decreases in C for the litter exclusion treatments appeared later, and were smaller than declines in root exclusion plots, highlighting the role of root detritus in the formation of soil organic matter in this forest. By year 8 of the experiment, surface soil C concentrations were lower than Control plots by 32% in NI, 23% in NR and 19% in NL. Increases in soil C in litter addition treatments were less than C losses from litter exclusion treatments, with surface C increasing by 12% in DL and 6% in DW. Detritus additions and removals had significant effects on soil microclimate, with decreases in seasonal variations in soil temperature (between summer and winter) in Double Litter plots but enhanced seasonal variation in detritus exclusion plots. Carbon dioxide (CO 2 ) emissions were most influenced by detritus input quantity and soil organic matter concentration when soils were warm and moist. Clearly changes in detritus inputs from altered forest productivity, as well as altered litter impacts on soil microclimate, must be included in models of soil carbon fluxes and pools with expected future changes in climate.

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Long‐term dynamics of phytoplankton have been addressed in marine and lake systems, but rarely in rivers. Large rivers, however, are highly human‐impacted, whereas global warming may further affect the functioning of phytoplankton at long‐term scale. In the middle section of the large European Danube River, long‐term decrease in phytoplankton biomass (Chl‐a) and increase in species diversity have formerly been revealed. The functional community composition that relates to ecosystem functioning directly has not been addressed previously. We analyse a 34‐year‐long phytoplankton data set from the middle river section at Göd (N‐Budapest), Hungary. We focus on gradual changes in the functional composition and functional diversity components based on the functional trait and functional group approaches. We hypothesised that long‐term gradual changes in major environmental constraints should be followed by gradual shifts in dominance relationships among functional traits and functional groups of phytoplankton. We further hypothesised that functional shifts were highlighted by gradual changes in functional diversity components: evenness, divergence and dispersion. Water discharge of the middle Danube shifted towards the more frequent occurrence of lower values. On the other hand, high floods (>3,000 m3/s) increased significantly with shortening tendency in duration and altered seasonality. The concentration of N and P forms, as well as total suspended solids decreased significantly. Water temperature increased significantly, especially in summer. In the phytoplankton, single‐celled eutrophic centric diatoms decreased in relative abundance, but flagellated, elongated and filamentous forms increased. A clear functional shift was the dominance decrease in planktonic taxa and the relative abundance increase in benthic diatoms. All functional diversity components increased significantly in the entire data set, except functional evenness (FEVE) based on the functional group approach. At seasonal scale, all significant trends showed increases, except the FEVE components of the functional group approach, which decreased in winter and spring significantly. Long‐term increase in functional diversity components alone could indicate enhanced ecosystem functioning of phytoplankton in the middle section of the Danube. However, we argue that the observed increase in functional diversity may be related to a gradual shift from high‐biomass communities with the dominance of eutrophic centric diatoms towards the relative increase in several, but low‐biomass elements. These include a few planktonic algae well adapted to the altered conditions, diatoms with benthic origin and dispersed limnophilic taxa. Our results provide the first evidence for a long‐term phytoplankton functional regime shift in a European large river. Global warming, human impacts and oligotrophication might potentially increase the functional diversity of large river phytoplankton, but the origin and functional role of taxa should carefully be considered. The ...

Effective management of water quality in large rivers requires information on the influence of activities within the catchment (urban and rural) throughout the whole river basin. However, traditional water quality monitoring programmes undertaken by individual agencies normally relate to specific objectives, such as meeting quality criteria for wastewater discharges, and fail to provide information on basin-scale impacts, especially in transboundary river basins. Ideally, monitoring in large international river basins should be harmonised to provide a basin-scale assessment of sources and impacts of human activities, and the effectiveness of management actions. This paper examines current water quality issues in the Danube River Basin and evaluates the approach to water quality monitoring in the context of providing information for a basin-wide management plan. Lessons learned from the monitoring programme in the Danube are used to suggest alternative approaches that could result in more efficient generation of water quality data and provide new insights into causes and impacts of variations in water quality in other large international river basins.