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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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

This study investigates the variations of polycyclic aromatic hydrocarbon (PAH) levels in surface water, suspended particulate matter (SPM) and sediment upstream and downstream of the discharges of two wastewater treatment plant (WWTP) effluents. Relationships between the levels of PAHs in these different matrices were also investigated. The sum of 16 US EPA PAHs ranged from 73.5 to 728.0 ng L(-1) in surface water and from 85.4 to 313.1 ng L(-1) in effluent. In SPM and sediment, ∑16PAHs ranged from 749.6 to 2,463 μg kg(-1) and from 690.7 μg kg(-1) to 3,625.6 μg kg(-1), respectively. Investigations performed upstream and downstream of both studied WWTPs showed that WWTP discharges may contribute to the overall PAH contaminations in the Loue and the Doubs rivers. Comparison between gammarid populations upstream and downstream of WWTP discharge showed that biota was impacted by the WWTP effluents. When based only on surface water samples, the assessment of freshwater quality did not provide evidence for a marked PAH contamination in either of the rivers studied. However, using SPM and sediment samples, we found PAH contents exceeding sediment quality guidelines. We conclude that sediment and SPM are relevant matrices to assess overall PAH contamination in aquatic ecosystems. Furthermore, we found a positive linear correlation between PAH contents of SPM and sediment, showing that SPM represents an integrating matrix which is able to provide meaningful data about the overall contamination over a given time span.