DOI: 10.5061/dryad.0cfxpnwb5
title: Data from: Reduced sampling intensity through key sampling site selection for optimal characterization of riverine fish communities by eDNA metabarcoding

description: Effective conservation management of river systems requires a
 comprehensive understanding of local and regional biodiversity,
 necessitating accurate characterization of species communities.
 Environmental DNA (eDNA) metabarcoding has emerged as a pivotal tool for
 assessing aquatic organisms, especially fish communities. However, optimal
 sampling resolution and site positioning to obtain robust fish diversity
 indices across heterogeneous river systems remain inadequately understood.
 This study empirically evaluates the optimal number of eDNA samples needed
 to accurately capture diversity both locally and stream-wide across three
 distinct river systems, comparing eDNA metabarcoding results to
 traditional electrofishing data. Habitat and landscape factors were
 characterized to interpret the localisation of key sampling sites
 contributing most to the overall species richness. We detected 30 fish
 species via eDNA metabarcoding, compared to 28 species by electrofishing,
 with eDNA requiring fewer sampling sites per river system. To reach ≥95 %
 of the estimated species richness, eDNA analyses required between one and
 nine sites across three river systems spanning ten kilometres each. In the
 most diverse river, a single eDNA sampling site even achieved a higher
 species richness (n = 20 species) compared to the nine required sites to
 reach ≥95 % of the estimated species richness via electrofishing (n = 9
 species). To account for eDNA particle dilution and degradation over
 larger distances (&gt;1 km), sampling at both upstream and downstream
 sites may be crucial, with strategic site selection further refined by
 factors like adjacent stream inflows, substrate type, and river discharge
 rate, all of which influence species-specific habitat occupancy. On a
 smaller scale, the location of key sampling sites only moderately differs
 within 100-meter transects therewith informing on the precise placement of
 those sampling sites. Our work highlights the robustness and
 cost-effectiveness of eDNA analyses for riverine biodiversity assessment,
 demonstrating strong potential for enhancing various conservation
 practices.
description: A comprehensive sampling campaign was conducted across 60 sites
 in the northern region of Belgium, spanning three rivers: Barbierbeek,
 Herk, and Berwinne. Each river was sampled on two spatial scales: ten
 100-meter transects for small-scale sampling and ten 100-meter sections at
 1-kilometer intervals for large-scale sampling. Per sampling site, water
 samples were taken, followed by electrofishing. The water samples were
 filtered and analysed using eDNA metabarcoding. This dataset includes the
 data of the eDNA metabarcoding as well as the raw fish count from the
 electrofishing activities. <br><br>Raw metabarcoding data was
 deposited on the NCBI's Sequence Read Archive (SRA) under BioProject
 number PRJNA1165199. 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 from: Reduced sampling intensity through key sampling site
 selection for optimal characterization of riverine fish communities by
 eDNA metabarcoding
 [https://doi.org/10.5061/dryad.0cfxpnwb5](https://doi.org/10.5061/dryad.0cfxpnwb5) ## Description of the data and file structure Dataset title: "Data from: Reduced sampling intensity through key sampling site selection for optimal characterization of riverine fish communities by eDNA metabarcoding" Principle investigator: Charlotte Van Driessche ([charlotte.vandriessche@inbo.be](mailto:charlotte.vandriessche@inbo.be)) Co-investigators: Teun Everts, Io Deflem, Sabrina Neyrinck, Dries Bonte, Rein Brys Data collection data: May, July 2023 Geographic location of data collection: Belgium, Flanders (Northern Region) ### Files and variables #### File: Data\_VanDriesscheEtAl\_key\_sampling.xlsx Creation data file: the 7th of October 2024 The dataset contains one tab page. 1\. Full: This is the full dataset already including electrofishing data, as well as eDNA generated fish detections, in both quantified (absolute, relative)as well as binary format.  Column explanations are listed below:  ID: an identification number for easy sorting of the data Method: detections arrise from either morphological identification (Fish) of via eDNA sampling (eDNA). The data was further given in an absolute number of reads or fish (absolute), a binary format (1 for presence, 0 for absence) or a relative contribution to the overall community (rel). If datapoint are given separate, a number 1 or 2 is added to the adequate 'Method', if both replicates are summarized into an average, 'Method' is followed by the 'av'_extension. FilterNo: If applicable, the filter code was given for the eDNA samples VolumeFilteredMl: The volume of water filtered to obtain the eDNA sample, given in ml Date: collection/sampling date Location: name of the studied river, followed by the distance of the river stransect compared to the river mouth RiverName: name of the studies river DistanceM: the distance (in m) from the river mouth where the transect was located RiverDischargeRate: rate of the river discharge in m3/s Slope: level of slope of the bottom of the river, subdivided into 'low-medium-high' levels of steepness Meander: number of clear meandering sections within the studied river section Agriculture: Y/N if agriculture took place at one or both of the riverbeds Industry: Y/N if Industrial activities took place at one or both of the riverbeds Substrate: bottom substrate, which was subdived into 'Mud-Rocks-Sand' ElectricConductivity: in µS/cm pH: level of pH if measured  WaterTemperature: in °C Turbidity: in NTU DissolvedOxygen: in mg/l TOTALReads: total number of reads for that filter, which is then used to calculate relative abundances for eDNA-based fish detections Remaining columns include the latin species names (scientific names) of the species identified morphologically and/or via eDNA sampling.  Missing values are listed as 'NA', equal to 'not available'. ## Access information This data was used generated in the Research Article (manuscript): Van Driessche, C., Everts, T., Deflem, I., Neyrinck, S., Bonte, D., & Brys, R. (2024) Reduced sampling intensity through key sampling site selection for optimal characterization of riverine fish communities by eDNA metabarcoding. *Ecological Indicators, 169, 112807. *[https://doi.org/10.1016/j.ecolind.2024.112807](https://doi.org/10.1016/j.ecolind.2024.112807)