A global systematic map of knowledge of inland commercial navigation effects on freshwater ecosystems.

Inland navigation is one of the most sustainable transport alternatives to help decarbonise the world economy. However, the likely impacts of intensifying inland navigation on freshwater ecosystems are difficult to predict. A global map of knowledge that considers both abiotic and biotic responses to increasing shipping traffic and developing infrastructures is lacking. Deriving general evidence-based assessments is challenging, because most studies on inland navigation impacts are merely descriptive and either consist of local case studies, or address single navigation stressors or specific taxa only. We conducted a systematic mapping of the published literature (1908-2021) to provide a global synthesis of the effects of inland navigation on the biotic and abiotic components of freshwater ecosystems. We show that only half of the reported navigation-related impacts were statistically tested. Navigation itself (vessel operation) had mainly negative effects on native taxa (57%), followed by waterway management (40%), and navigation infrastructures (35%). Navigation has direct negative impacts caused by physical disturbances such as vessel-induced waves, and indirect impacts that facilitate the spread of aquatic invasive species, and altering the abiotic habitat conditions. Thirty percent of the tested relationships showed non-significant impacts on the biotic environment, while in 10% of cases impacts were context-dependent. We identified the main gaps of knowledge, namely (i) impacts of waterway management on communities, (ii) underlying processes of navigation impacts on river ecosystems; and (iii) interactions between multiple navigation factors and cascading effects on multi-taxa responses. These future research directions should improve the diagnosis, mitigate the negative impacts of navigation on rivers and provide guidelines for improving navigated river management.

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.

Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding.

As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.

Water temperature dynamics in a headwater forest stream: Contrasting climatic, anthropic and geological conditions create thermal mosaic of aquatic habitats.

The thermal regime of streams is a relevant driver of their ecological functioning. As this regime is presently submitted to numerous alterations (among others, impoundments, and climate change), it seems important to study both their effects and potential recovery from the latter. Thus, we investigated the surface and hyporheic water temperature along a small headwater stream with contrasting environmental contexts: forest landscape, open grassland landscape without riparian vegetation, several artificial run-of-the-river impoundments and one discharge point of a by-pass impoundment. The main objectives were to study the influence of these contrasting contexts on surface and subsurface water temperature at a local scale. Contrasting contexts were supposed to create effects on both surface and hyporheic thermal regimes at a local scale. Differences of thermal regimes between surface and hyporheos were expected, as well as between geological contexts. Sensors located at multiple stations allowed monitoring of stream and hyporheos temperature along the stream, while comparison with adjacent reference stream allowed for surface water thermal regime benchmark. Impoundments and landscapes significantly influenced stream thermal regime at a local scale (impoundments created up to +3.7°C temperature increase in average). Their effect on hyporheos thermal regime was less marked than the ones generated by solar radiation or geological features. Hyporheos thermal regime varies from stream one by temperature dynamics delay (up to 18h) and decrease (up to -7°C between surface and hyporheos temperature in average). These coupled effects create a mosaic of thermal habitats, which could be used for river biodiversity preservation and restoration.

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.

Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering.

Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.

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.

High food quality increases infection of Gammarus pulex (Crustacea: Amphipoda) by the acanthocephalan parasite Pomphorhynchus laevis.

Parasitism is an important process in ecosystems, but has been largely neglected in ecosystem research. However, parasites are involved in most trophic links in food webs with, in turn, a major role in community structure and ecosystem processes. Several studies have shown that higher nutrient availability in ecosystems tends to increase the prevalence of parasites. Yet, most of these studies focused on resource availability, whereas studies investigating resource quality remain scarce. In this study, we tested the impact of the quality of host food resources on infection by parasites, as well as on the consequences for the host. Three resources were used to individually feed Gammarus pulex (Crustacea: Amphipoda) experimentally infected or not infected with the acanthocephalan species Pomphorhynchus laevis: microbially conditioned leaf litter without phosphorus input (standard resource); microbially conditioned leaf litter enriched in phosphorus; and microbially conditioned leaf litter without phosphorus input but complemented with additional inputs of benthic diatoms rich in both phosphorus and eicosapentaenoic acid. During the 110 day experiment, infection rate, parasite load, host survival, and parasite-mediated behavioral traits implicated in trophic transmission were measured (refuge use, geotaxis and locomotor activity). The resources of higher quality, regardless of the infection status, reduced gammarid mortality and increased gammarid growth. In addition, higher quality resources increased the proportion of infected gammarids, and led to more cases of multi-infections. While slightly modifying the geotaxis behavior of uninfected gammarids, resource quality did not modulate the impact of parasites on host behavior. Finally, for most parameters, consumption of algal resources had a greater impact than did phosphorus-enriched leaf litter. Therefore, manipulation of resource quality significantly affected host-parasite relationships, which stressed the need for future research to investigate in natura the relationships between resource availability, resource quality and parasite prevalence.

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.