Data from: 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.