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 monitoring, we simultaneously combine stow net fishing with eDNA metabarcoding, to assess the Scheldt estuary's fish communities in space and time. In total, we detected 71 fish species in the estuary using eDNA metabarcoding, partly overlapping with historic fish community data gathered at the different study locations and in contrast to only 42 species using stow net fishing during the same survey period. Community compositions found by both detection methods varied amongst sampling locations, driven by a clear correlation to the salinity gradient. Limited effects of sampling depth and tide were observed on the eDNA metabarcoding data, allowing a significant reduction of the eDNA sampling effort for future eDNA fish monitoring campaigns in this study system. Our results further demonstrate that seasonal shifts in fish species occurrence can be detected using eDNA metabarcoding. Combining eDNA metabarcoding and stow net fishing further enhances our understanding of this vital waterway’s diverse fish populations, allowing a higher resolution and more efficient monitoring strategy.

Methods
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 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.