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Providing reliable, cost‐effective data on species distribution is critical to ensuring biodiversity conservation. However, many species may go unrecorded by conventional surveys, especially in aquatic environments. Environmental DNA (eDNA) barcoding and metabarcoding are alternative approaches that could complete biodiversity estimates based on species observations. While eDNA surveys are being standardized for some animal groups (e.g., fish and amphibians), research on eDNA approaches for freshwater plant communities is just starting to bear fruit. Here, we synthesized the 22 studies that used eDNA barcoding and metabarcoding to survey plant biodiversity in freshwater systems. We present evidence that contemporary aquatic plants (macrophytes) and terrestrial plants can be detected in water and surficial sediment eDNA from lakes and rivers. The phenology (e.g., senescence) of the target taxa strongly influences species detection. The main application of eDNA barcoding targets the monitoring of invasive macrophytes, and barcoding assays are available for 14 taxa. The metabarcoding approach shows a range of applications: the detection of rare macrophytes, catchment‐scale floristic inventories, and sediment fingerprinting. Barcodes on the plastid genome (cpDNA) are preferred for both approaches: matK and trnH‐psbA for barcoding, trnL, and rbcL for metabarcoding. The intergenic transcribed spacer 1 (ITS1) from the nuclear ribosomal DNA (nrDNA) was used for designing eDNA barcoding assays on five invasive macrophytes. In contrast, only three metabarcoding studies used the ITS1 or IST2 with newly designed primers. However, metabarcoding applications should routinely use a multi‐locus approach, combining cpDNA and nrDNA barcodes. Barcode combinations and existing primers need further testing on eDNA samples. We recommend using local barcode reference databases (BRDs), ideally self‐made, to circumvent taxonomic gaps and heterogeneous sequences in public BRDs. Finally, new technologies and developments like droplet digital PCR and hybridisation capture offer new perspectives for eDNA‐based biodiversity monitoring approaches. In this manuscript we present a synthesis of the 22 studies working on eDNA barcoding and metabarcoding approaches for monitoring freshwater plants in lentic, lotic and wetland habitats. We also examine the specific primers, barcodes and reference databases required for succesful plant eDNA surveys.

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.

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.

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

Due to their high filtration rates, exotic freshwater bivalves remove suspended organic matter from the water column, transferring resources to the sediment and increasing water clarity, which alters ecosystems. While there is a considerable amount of data on filtration rate of exotic bivalves, comparison between species is often invalid due to the utilization of different protocols for assessing filtration in experimental conditions. In this study, we quantified and compared for the first time the filtration rates of the zebra and quagga mussels and of two invasive Corbicula lineages (forms R and S) as a function of chlorophyll a concentration and season. The highest filtration rate observed was for the zebra mussel in fall and at high algal biomass. The incipient limiting level (ILL), defined as the chlorophyll a concentration at which the maximum filtration rate is observed, was observed in spring and summer in Corbicula species, and in summer and fall in Dreissena species. Overall, filtration rates presented a large range of variation, depending on chlorophyll a and season. Overall, Corbicula form S was observed as the best adapted to low food concentration. Moreover, Corbicula can switch to pedal feeding which gives them a competitive advantage at low chlorophyll a concentrations.

The quagga mussel (Dreissena rostriformis bugensis) is an invasive alien species present in many aquatic ecosystems. Although this species is known for its ecological and economic impacts, there are still significant gaps in our knowledge of its ecophysiology. This is particularly true when its growth rate under natural conditions is considered. Using a photogrammetry-based approach, we assessed bivalve growth in Lake Geneva during different seasons and for a variety of habitats. Based on the recorded changes in maximum shell length analysed during the period of this study (winter and spring 2023-2024), we measured average growth rates ranging from 0.142 ± 0.099 mm day -1 for individuals smaller than 10 mm to 0.089 ± 0.071 mm day -1 for larger individuals. The size class-dependent growth rate was analysed on the basis of the time of year, the type of environment (depth, substrate) or, again, the temperature. Our results reveal that the growth rate, obtained in situ and without manipulation, primarily depends on size and is independent of temperature or habitat within the studied range. This growth capacity in Lake Geneva is the highest found to date and is likely to explain the invasion success of this species.

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.

Deformities and fluctuating asymmetry in chironomid larvae have been proposed as sensitive indicators of biological stress and are commonly used to assess the ecological impact of human activities. In particular, they have been associated in Chironomus riparius, the most commonly used species, with heavy metal and pesticide river pollution. In this study, the effect of lead and 4-nonylphenol on mouthpart morphological variation of Chironomus riparius larvae was investigated by traditional and geometric morphometrics. For this purpose, first to fourth instar larvae were exposed to sediment spiked with lead (from 3.0 to 456.9 mg/kg dry weight) or 4-NP (from 0.1 to 198.8 mg/kg dry weight). Mentum phenotypic response to pollutants was assessed by four parameters: (1) the frequency of deformities, (2) fluctuating asymmetry of mentum length, (3) fluctuating asymmetry of mentum shape and (4) the mentum mean shape changes. Despite the bioaccumulation of pollutants in the chironomid's body, no significant differences between control and stressed groups were found for mouthpart deformities and fluctuating asymmetry of mentum length. Slight effects on mentum shape fluctuating asymmetry were observed for two stressed groups. Significant mean shape changes, consisting of tooth size increase and tooth closing, were detected for lead and 4-NP exposure respectively. Those variations, however, were negligible in comparison to mentum shape changes due to genetic effects. These results suggest that the use of mentum variation as an indicator of toxic stress in Chironomus riparius should be considered cautiously.

Trophically-transmitted parasites are known for their ability to enhance predation of their intermediate host but they are less known for their ability to suppress predation. We review recent literature on host manipulation explaining why and when in its life cycle a parasite benefits from preventing the predation of its host. Predation suppression occurs in intermediate hosts as long as the parasite larva has not reached the developmental conditions allowing it to successfully establish in the next host (competency). We also examine the possibility that predation suppression may occur in hosts harbouring competent larvae (post competency) since some parasites have been shown to manipulate host behaviour in a way that decreases the risk of parasite death through non-host predation (i.e. the consumption of its intermediate host by a predator that does not risk infection). Predation suppression when the parasite is competent has to be considered with respect to non-host predation risk and is not mutually exclusive with predation enhancement. We use the recent theoretical advances in host manipulation to investigate the conditions under which predation suppression could evolve post competency.

Despite their ecological importance, mosses remain under-represented in ecological studies due to their challenging detection in field surveys and morphological identification, exacerbated by the lack of expert botanists. In this study, we optimise an environmental DNA method for the detection of bryophytes from river water samples, with the aim of facilitating their inclusion in biodiversity assessments. We compared three different methods in terms of species detection and community dissimilarity at seven sites along a river. The methods include (i) visual transect surveys conducted by bryologists based on macro- and micro-morphology, (ii) multi-marker PCR metabarcoding of the rbc L and the ITS2 markers with newly designed primers targeting bryophytes, and (iii) hybridisation capture (HC) for the same markers. We found that PCR metabarcoding recovered more than 50% (n = 37) of the species observed in the field, while hybridization capture detected only 16% (n = 11). PCR metabarcoding identified the most species, 101 species compared to 68 observed in the field and 27 with HC. Both the PCR and HC metabarcoding approaches identified bryophyte species not recorded in field surveys but expected in the catchment. Molecular methods, particularly PCR metabarcoding, recovered rare and elusive species difficult to observe in the field and occurring outside our transect. The two markers used in the molecular approaches contributed uniquely to species detection, making a multi-marker approach necessary to study this group. Environmental DNA and field surveys represent integrative methods that collectively enhance detection of inconspicuous species and yield the most comprehensive species inventory.