A comparative analysis of eDNA metabarcoding and field surveys: Exploring freshwater plant communities in rivers.

While environmental DNA (eDNA) metabarcoding holds promise as a holistic approach to assess vegetation changes and community composition across diverse spatial and temporal scales, systematic investigations of its efficacy compared to conventional field surveys remain scarce in the literature. The present study explores the differences in plant diversity recovered from field surveys and captured with a multi-marker eDNA metabarcoding approach (two nrDNA ITS1 and ITS2, and two cpDNA rbcL and trnL) from river water samples. The eDNA metabarcoding approach retrieved 46 aquatic plants (hydrophytes and helophytes) and 245 terrestrial plants, compared to 24 and 127 species identified from field surveys. On average, eDNA samples collected immediately downstream of the survey sites recovered 43 % and 39 % of the aquatic and terrestrial species observed, respectively. Discrepancies were explained by differences in taxonomic resolution, the stochasticity of the retrieval of rare and elusive species, and the presence of reference sequences. We found a significant positive correlation between spatial and community distances at scales ranging from 2 to 9 km and identified turnover as the driving force of these differences. Metabarcoding demonstrated sensitivity to community changes and both approaches converge on a similar community structure. Interestingly, eDNA samples collected immediately upstream of the survey sites exhibited significant species overlap with the downstream samples (c. 100 m apart). Overall, our results demonstrate that within-site species mismatches between the methods are nonnegligible, and they question the use of eDNA for generating complete species lists at scales comparable to our field surveys (< 100-m transects). However, with adequate sampling and a multi-marker metabarcoding approach, eDNA has the potential to approximate catchment gamma diversity with less sampling effort than conventional surveys.

Inland navigation and land use interact to impact European freshwater biodiversity.

Inland navigation in Europe is proposed to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this would impact biodiversity at large scales and interact with existing stressors. Here we addressed this knowledge gap by analysing fish and macroinvertebrate community time series across large European rivers comprising 19,592 observations from 4,049 sampling sites spanning the past 32 years. We found ship traffic to be associated with biodiversity declines, that is, loss of fish and macroinvertebrate taxonomic richness, diversity and trait richness. Ship traffic was also associated with increases in taxonomic evenness, which, in concert with richness decreases, was attributed to losses in rare taxa. Ship traffic was especially harmful for benthic taxa and those preferring slow flows. These effects often depended on local land use and riparian degradation. In fish, negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was evident only when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian habitats and landscape characteristics could help to mitigate these impacts.

Evolution of relict floodplain forest in river stretches of Western and Central Europe as affected by river infrastructure networks.

We studied the impact of infrastructure networks on relict floodplain forest along three stretches of the Upper Rhine (Kembs-Efringen-Kirchen, Strasbourg-Kehl and Beinheim-Iffezheim) and the Inn-Danube (Mulheim-Obernberg, Passau-Ingling and Engelhartszell-Jochenstein), each on the border between two countries. We analysed land use patterns within a 500 m wide buffer area along the main channel using photo-interpretation and compared the situations between the 1950s, 1980's and 2010's. Temporal changes were assessed with transition matrices and selected spatial metrics, including fragmentation indices. Over this period, forest area remained similar at three sites, increased slightly at two sites and decreased at one site. However, on average, 12.5% of floodplain forest had changed location (range: 7.3% (Engelhartszell-Jochenstein)- 26.5% (Kembs-Efringen-Kirchen)). The natural development of unmanaged areas and agricultural abandonment after World War II has led to the emergence of young riparian forests along rivers. In the Upper Rhine region, the results showed asymmetry in these two factors, with unmanaged natural areas most important on the French side and agricultural abandonment on the German side. Along the Inn-Danube, agricultural abandonment has led to an increase or stagnation of floodplain forest areas. In most cases, development of transport infrastructure between the 1950s and 2010s has caused fragmentation of the forest area, reducing the relict forest to a patchy green corridor with reduced functionality and interfacing. To go further and improve the management of these relict forests, we have to investigate the interdependency between practices related to infrastructure operation and the role that biodiversity plays for stakeholders.

Restoring fluvial forms and processes by gravel augmentation or bank erosion below dams: A systematic review of ecological responses.

Aquatic biological communities have directly undergone human-induced changes. Altered hydrological and morphological processes in running waters have caused the degradation of main habitats for biotas and have disturbed ecosystem functionality. The latest advances in river restoration concerned the rise in far-reaching hydromorphological restoration actions that have been implemented below dams to reverse well-known negative impacts of anthropogenic pressures. Some authors emphasized the enhancement of sediment supply and habitat diversity using gravel augmentation or bank erosion to restore morphodynamics, and thus improve biodiversity. We explored the Web of Science database for empirical research papers that specifically addressed such hydromorphological river restoration actions. Articles were examined using a text-content analysis tool to determine the major concepts or ideas they deal with. It has also been proved as useful in defining interrelationships and degree of interdisciplinary. Results showed that a low number of published scientific articles exist about such projects, mainly condensed in the North hemisphere. Divergent ecological issues were highlighted by the word co-occurrence networks: (i) gravel augmentation was used to improve spawning habitats for fish of economic interest whereas (ii) erodible corridor was designed to safeguard natural riparian systems, approaching morphological goals of channel widening. Overall, ecological responses were consistent with those expected, leading however rather to functional shifts than richness increase. Gravel augmentation or bank erosion were not usually combined with in-channel structure management. However, this might be an option to consider since the biological communities seem to be sensitive during first restorations with such combination. This review demonstrates the value of word co-occurrence networks in exploring a high number of previous publications, keys for formulating guidance to manage gravel augmentation or bank erosion along ecological purposes.

A minimalist macroparasite diversity in the round goby of the Upper Rhine reduced to an exotic acanthocephalan lineage.

The round goby, Neogobius melanostomus, is a Ponto-Caspian fish considered as an invasive species in a wide range of aquatic ecosystems. To understand the role that parasites may play in its successful invasion across Western Europe, we investigated the parasitic diversity of the round goby along its invasion corridor, from the Danube to the Upper Rhine rivers, using data from literature and a molecular barcoding approach, respectively. Among 1666 parasites extracted from 179 gobies of the Upper Rhine, all of the 248 parasites barcoded on the c oxidase subunit I gene were identified as Pomphorhynchus laevis. This lack of macroparasite diversity was interpreted as a loss of parasites along its invasion corridor without spillback compensation. The genetic diversity of P. laevis was represented by 33 haplotypes corresponding to a haplotype diversity of 0·65 ± 0·032, but a weak nucleotide diversity of 0·0018 ± 0·00015. Eight of these haplotypes were found in 88·4% of the 248 parasites. These haplotypes belong to a single lineage so far restricted to the Danube, Vistula and Volga rivers (Eastern Europe). This result underlines the exotic status of this Ponto-Caspian lineage in the Upper Rhine, putatively disseminated by the round goby along its invasion corridor.