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This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden. The course was co-organized by the EU COST research network DNAqua-Net and the SLU Research Schools Focus on Soils and Water (FoSW) and Ecology - basics and applications. DNAqua-Net (COST Action CA15219, 2016-2020) is a network connecting researchers, water managers, politicians and other stakeholders with the aim to develop new genetic tools for bioassessment of aquatic ecosystems in Europe and beyond. The PhD course offered a comprehensive overview of the paradigm shift from traditional morphology-based species identification to novel identification approaches based on molecular markers. We covered the use of molecular tools in both basic research and applied use with a focus on aquatic ecosystem assessment, from species collection to the use of diversity in environmental legislation. The focus of the course was on DNA (meta)barcoding and aquatic organisms. The knowledge gained was shared with the general public by creating Wikipedia pages and through this collaborative Open Access publication, co-authored by all course participants.

Riparian zones form the interface between stream and terrestrial ecosystems and play a key role through their vegetation structure in determining stream biodiversity, ecosystem functioning and regulating human impacts, such as warming, nutrient enrichment and sedimentation. We assessed how differing riparian vegetation types influence the structural and functional composition (based on species traits) of stream invertebrate communities in agricultural catchments. We characterized riparian and stream habitat conditions and sampled stream invertebrate communities in 10 independent site pairs, each comprising one “unbuffered” reach lacking woody riparian vegetation and a second downstream reach with a woody riparian buffer. Forested riparian buffers were associated with greater shading, increased gravel content in stream substrates and faster flow velocities. We detected changes in invertebrate taxonomic composition in response to buffer presence, with an increase in sensitive Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa and increases in key invertebrate species traits, including species with preference for gravel substrates and aerial active dispersal as adults. Riparian vegetation independently explained most variation in taxa composition, whereas riparian and instream habitat together explained most variation in functional composition. Our results highlight how changes in stream invertebrate trait distributions may indirectly reflect differences in riparian habitat, with implications for stream health and cross-ecosystem connectivity.

Riparian habitats are important ecotones connecting aquatic and terrestrial ecosystems, but are often highly degraded by human activities. Riparian buffers might help support impacted riparian communities, and improve trophic connectivity. We sampled spider communities from riparian habitats in an agricultural catchment, and analyzed their polyunsaturated fatty acid (PUFA) content to quantify trophic connectivity. Specific PUFAs are exclusively produced by stream algae, and thus are used to track uptake of aquatic resources by terrestrial consumers. Riparian spiders were collected from 10 site pairs situated along agricultural streams, and from five forest sites (25 sites total). Each agricultural site pair comprised an unshaded site with predominantly herbaceous vegetation cover, and a second with a woody riparian buffer. Spider communities differed between site types, with web-building spiders dominating woody buffered sites and free-living spiders associated with more open habitats. PUFA concentrations were greatest overall in free-living spiders, but there was also evidence for increased PUFA uptake by some spider groups when a woody riparian buffer was present. Our results reveal the different roles of open and wooded riparian habitats in supporting terrestrial consumers and aquatic-terrestrial connectivity, and highlight the value of incorporating patches of woody vegetation within riparian networks in highly modified landscapes.

Developing a general, predictive understanding of ecological systems requires knowing how much structural and functional relationships can cross scales and contexts. Here, we introduce the CROSSLINK project that investigates the role of forested riparian buffers in modified European landscapes by measuring a wide range of ecosystem attributes in stream-riparian networks. CROSSLINK involves replicated field measurements in four case-study basins with varying levels of human development: Norway (Oslo Fjord), Sweden (Lake Mälaren), Belgium (Zwalm River), and Romania (Argeş River). Nested within these case-study basins include multiple, independent stream-site pairs with a forested riparian buffer and unbuffered section located upstream, as well as headwater and downstream sites to show cumulative land-use impacts. CROSSLINK applies existing and bespoke methods to describe habitat conditions, biodiversity, and ecosystem functioning in aquatic and terrestrial habitats. Here, we summarize the approaches used, detail protocols in supplementary materials, and explain how data is applied in an optimization framework to better manage tradeoffs in multifunctional landscapes. We then present results demonstrating the range of riparian conditions present in our case-study basins and how these environmental states influence stream ecological integrity with the commonly used macroinvertebrate Average Score Per Taxon (ASPT) index. We demonstrate that a qualitative index of riparian integrity can be positively associated with stream ecological status. This introduction to the CROSSLINK project shows the potential for our replicated study with its panoply of ecosystem attributes to help guide management decisions regarding the use of forested riparian buffers in human-impacted landscapes. This knowledge is highly relevant in a time of rapid environmental change where freshwater biodiversity is increasingly under pressure from a range of human impacts that include habitat loss, pollution, and climate change.