Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary

Estuarine ecosystems face increasing anthropogenic pressures, necessitating effective monitoring methods to mitigate their impacts on the biodiversity they harbour. The use of environmental DNA (eDNA) based detection methods is increasingly recognized as a promising tool to complement other, potentially invasive monitoring techniques. Integrating such eDNA analyses into monitoring frameworks for large spatial ecosystems is still challenging and requires a deeper understanding of the scale and resolution at which eDNA patterns may offer insights in species presence and community composition space and time. The Scheldt estuary, characterized by its diverse habitats and complex currents, is one of the largest Western European tidal river systems. Until now, it remains challenging to obtain accurate information on fish communities living in and migrating through this large ecosystem, consequently confining our knowledge to specific locations. To explore the potential of eDNA-based monitorin..., A large-scale seasonal sampling campaign combining stow net fishing and environmental DNA (eDNA) sampling was performed in the Scheldt estuary. During three seasons (spring, summer, autumn), fish communities were investigated at four different sampling sites in Belgium (Doel, Antwerp, Steendorp, Branst). Per sampling site, fishing was performed with two stow nets during low tide, and during high tide. Per fishing haul (so twice per tide), three eDNA samples were taken, once per depth level (i.e. deep, middle or surface) of the water column using a Von Dorn sampler. Water samples were analysed using eDNA metabarcoding. This dataset includes the data of the stow net fishing as well as the read counts of the eDNA metabarcoding.
Raw metabarcoding data was deposited on the NCBI’s Sequence Read Archive (SRA) under BioProject number PRJNA1065114. The bioinformatical pipeline as used on these raw read counts is available on Zenodo (https://zenodo.org/record/3731310#.Y8pdbXbMI2w). The OBITools s..., , # Data from: Environmental DNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary

**I. General information**

Dataset title: \"Data from: eDNA metabarcoding reflects spatiotemporal patterns of fish community shifts in the Scheldt estuary\"

Principle investigator: Charlotte Van Driessche ([[e-mail]](mailto:[e-mail]))

Co-investigators: Teun Everts, Sabrina Neyrinck, David Halfmaerten, Pieter Verschelde, Jan Breine, Dries Bonte, Rein Brys

Data collection data: April, July, September 2021

Geographic location of data collection: Belgium, Flanders (Northern Region)

Keywords: biodiversity monitoring, integrated sampling, assay sensitivity, reference database, salinity, seasonal migration

Principal funders: Research Foundation Flanders grants for strategic basic research (FWO-SB, grant number 1S23822N to CVD and grant number 1S01822N to TE) and the Research Institute for Nature and Forest

As a result o...