Drewitt, A. | bioRxiv Science

bioRxiv2025

Multi-seasonal eDNA metabarcoding highlights a resurgence in fish diversity across a severely impacted estuarine ecosystem

Aquatic ecosystems have been in an alarming state of decline for decades. Therefore, there is an urgent need for more accessible and rapid monitoring methods that will ultimately allow for restoration programmes to be implemented. In this study, we deployed environmental DNA (eDNA) metabarcoding as a fish monitoring tool in the Mersey estuarine system (UK), where ecosystem productivity has been severely impacted by water quality degradation since the Industrial Revolution. Monthly water samples were collected over a year (2023-2024) throughout the estuary, covering saline, brackish and freshwater zones. Overall, 69 species of fish were detected, increasing the number of known species within the estuary in comparison to both historical and contemporary records (46 and 39, respectively), with a generally higher observed richness within the upper estuary sampled zones where the water chemistry is predominantly freshwater. Notably, we identified several species returning to the system for the first time since pre-industrial times. Peak species richness was recorded during the winter season (December-February). Species compositions varied significantly by month and spatially by zone within months, but not when grouped seasonally. Furthermore, around [~]15% of the species detected were diadromous, with the endangered Atlantic salmon Salmo salar, for example, being frequently detected during its key migratory period. This study highlights the resurgence in fish diversity in a once biologically depleted estuarine ecosystem and demonstrates how eDNA metabarcoding can be implemented for detecting historically absent species, thereby enhancing restoration monitoring efforts globally.

ecology↗

bioRxiv2024

Performance of eDNA capture methods for monitoring fish biodiversity in a hyper-tidal estuary

Environmental DNA (eDNA) has become an established and efficient method for monitoring biodiversity in aquatic systems. However, there is a need to compare and standardise sampling methods across ecosystem types, particularly complex ecosystems such as estuaries where unique challenges for monitoring fish populations are present due to fluctuating environmental factors. Here, we compare fish biodiversity metrics obtained from eDNA metabarcoding data using four different eDNA filtering methods: three manual filtering methods with different pore sizes (0.45, 1.2 and 5 {micro}m) and a newly established passive method, the metaprobe. The study was applied across a salinity gradient in a hyper-tidal estuarine ecosystem. Overall, 44 fish species were detected across the four methods used. The 0.45 {micro}m filter recovered the highest richness (39 species), then the metaprobe method (35), followed by the 1.2 {micro}m (34) and 5 {micro}m (33) filters. Filter performance between salinity gradients revealed that the 0.45 {micro}m and the 1.2 {micro}m methods recovered the highest species richness across all sampled zones. The 0.45 {micro}m also had the most consistent detection probabilities using representative species from each zone. While the 0.45 {micro}m method appeared to be the optimal method, each of the methods can be considered as a viable and comparable option for biomonitoring in dynamic ecosystems such as estuaries and rivers. In particular, the passive metaprobe (used in a freshwater system for the first time here) performed well in comparison to the manual filtering methods despite a short deployment time. This study provides critical insights for optimising fish biodiversity assessments using eDNA metabarcoding in estuarine ecosystems, providing a valuable framework for future monitoring efforts in similar systems worldwide.

molecular biology↗