DOI: 10.5061/dryad.tx95x6b2n
title: Data from: Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information

description: Monitoring fish communities is central to the evaluation of ecological
 health of rivers. Not only presence/absence of species is important to
 assess, but also the species composition of local fish assemblages is a
 crucial parameter. Lotic fish communities are traditionally monitored via
 electrofishing, characterized by a known limited efficiency and high
 survey costs. The use of environmental DNA-based analyses could serve as a
 non-destructive alternative, but this approach requires further insights
 in practical sampling schemes incorporating transport and dilution of the
 eDNA fragments; as well as optimization of molecular detection in terms of
 predictive power and quality assurance. By introducing fifteen species
 known to occur in Belgian waters via a controlled cage experiment, we aim
 to extend the knowledge on streamreach of eDNA in small rivers and large
 brooks, as laid out in the European Water Framework Directive’s water
 typology. Introducing fish communities in two transects of a species poor
 river characterized by contrasting river discharge rates, we found strong
 and significant correlations between the eDNA relative abundances and the
 relative biomass per species in the cage community. Despite a decreasing
 correlation over distance, the underlying community composition remained
 stable over a distance of 300 m up to 1 km downstream of the cages,
 depending on the river discharge rate. Such decrease in similarity between
 relative source biomass and the corresponding eDNA-based community profile
 with increasing distance downstream from the source, can partly be
 attributed to variation in species-specific eDNA persistence. Our findings
 offer novel insights on eDNA behaviour and characterization of riverine
 fish communities. We conclude that water sampled from a relatively small
 river offers an adequate snapshot of the total fish community composition
 occurring within an upstream perimeter ranging between 300 and 1000
 meters. The potential application for other river systems is discussed in
 this study.
description: A controlled cage experiment
 was performed. Fifteen fish species were held in keepnets (~cages) in a
 small river in Belgium. At varying distances downstream from the nets,
 water samples were taken. Environmental DNA was extracted and samples were
 analysed via both droplet digital PCR (see Van Driessche et al., 2022) as
 well as via eDNA metabarcoding. This dataset includes the data of the eDNA
 metabarcoding. The entire set-up was repeated in two river transects with
 contrasting river discharge rates. Two levels of source fish biomass were
 used. Raw data was deposited on the NCBI’s Sequence
 Read Archive (SRA) under BioProject number PRJNA904931. The
 bioinformatical pipeline as used on these raw read counts is available on
 Zenodo (https://zenodo.org/record/3731310#.Y8pdbXbMI2w). The OBITools
 software was used for further processing of the generated sequence data.
 The resulting count table as available here was used for further quality
 screening and cleaning, as well as for statistical analyses.
description: Data can best be accessed using Microsoft Excel
 and R.