Using environmental DNA metabarcoding to monitor fish biodiversity and assess anthropogenic barrier impacts on the river Mersey, UK

Perkins, JC

Abstract

Freshwater habitats, despite their limited volume, support almost 10% of global biodiversity and are facing increased anthropogenic threats worldwide. Dams and weirs, for example, create habitat fragmentation, changing water flow and water levels, blocking crucial nutrients passing through river systems, and, above all, preventing crucial movements and migrations of aquatic organisms. Fish passes alleviate the problem, increasing river connectivity, but there is an evident need for a better understanding of their efficiency for fish movements and migration. Monitoring aquatic systems is notoriously difficult and traditional methods such as electrofishing and trapping can be invasive, costly and not always effective. The use of a novel molecular approach, environmental DNA (eDNA) metabarcoding, is now revolutionising biomonitoring. In this thesis, data collected from non-invasive monitoring techniques (camera recordings and eDNA metabarcoding) were combined to monitor Atlantic salmon migration at the Woolston weir fish pass, on the river Mersey, UK. In addition, a fine-scale spatial-temporal sampling approach was employed to investigate changes in fish communities below and above two weirs, from the Mersey estuary to the upper Mersey, in autumn and spring. Atlantic salmon was detected above and below Woolston weir, showing a good degree of connectivity and demonstrating the power of eDNA metabarcoding in detecting even few individuals (as revealed from the camera data). In total, 30 species were detected, including all main UK migratory species except for shad. Temporal variation was found in the detected communities, in line with expectations of different species’ migratory patterns. No correlation was found between barriers and community composition along the river, although lower species richness was detected at sites directly above each weir. Highest species richness was found at sampling sites at the geographical border of the lower and upper estuary, possibly due to tidal and river flow combination, suggesting that these types of environments could be optimal sampling areas to monitor the whole river biodiversity at once. Environmental parameters (pH, oxygen, salinity and temperature) were also integrated in the analyses. For example, the salmonid species showed a positive relationship with oxygen, and are known to require well oxygenated water to spawn. Overall, this work reinforces the potential of eDNA metabarcoding for ongoing and future biomonitoring efforts of fish communities (including migratory species) in a recovering river.

Citation

Perkins, J. Using environmental DNA metabarcoding to monitor fish biodiversity and assess anthropogenic barrier impacts on the river Mersey, UK. (Dissertation). University of Salford

• Thesis Type: Dissertation
• Deposit Date: Oct 7, 2020
• Publicly Available Date: Oct 7, 2020
• Award Date: Sep 22, 2020