Developing eDNA approaches for the detection of European smelt (Osmerus eperlanus) on the River Wyre.
Abstract
The European smelt, Osmerus eperlanus is a small anadromous fish which largely occupies coastal and brackish waters and moves into freshwater for spawning. Historically, Osmerus eperlanus was an important and abundant key species in many estuarine fisheries across the UK and Northern Europe. In the 1600's it was not uncommon for 50000 fish per day to be landed at Deptford Creek on the Thames. The fish was one of the first to receive legal protection in 1630 after Sir Robert Dulcie forbade smelt fishing to protect the smelt as they made their spawning run up the River Thames and throughout the heart of London. Unfortunately, this could not prevent population decline and by the 1870's the species was becoming scarce in the Thames. This trend was mirrored across the country as pollution and overfishing decimated rivers and the species which had resided within them. The main aims of the study were to obtain a DNA barcode of smelt, develop primers for single species eDNA smelt detection and analyse water samples for Smelt DNA presence. From this paper, Natural England and UHI were able to establish evidence that eDNA based approaches are highly suitable for assessing spatio-temporal distribution of UK smelt populations in estuaries and coastal freshwater. Additionally, the species specific assay developed here is highly promising, providing at comparable costs, a slightly higher detection probability for European smelt. The fish (N=54) fish were analyzed for qPCR assay, and eDNA metabarcoding quality control wherein results showed for qPCR screening of eDNA samples showed that 30 out of 54 samples tested positive for smelt eDNA with the number of positive replicates per positive sample ranging from 1-10 out of 10. The smelt DNA concentrations in the eDNA extractions ranged from 0.00006 to 0.023805 ng/ul per sample, as an average across the 10 replicates. Taking into account variations in filtration volume this translated into 0.2ng - 4.0ng per litre of water. Smelt eDNA concentrations were highest at the putative spawning sites and peaked at the last day of sampling, 28th March 2022. No positive detection was recorded at the control side upstream of the spawning locations. For eDNA metabarcoding: A total of 23 out of 54 samples tested positive for smelt eDNA with the number of smelt sequence reads per sample ranging from 14 - 8868. The relative proportion of smelt sequence reads from all fish sequence reads ranged from 0.001 to 0.2 per sample. Smelt eDNA concentrations were highest at the putative spawning sites and peaked at the last day of sampling, 28th March 2022. No positive detection was recorded at the control side upstream of the spawning locations. Based on the results of this small-scale study eDNA based approaches appear a highly suitable tool to monitor the spatio-temporal distribution of smelt in UK estuarine and freshwaters. The species-specific assay developed here is a very promising and cost effective approach which provides at comparable costs/sample a slightly higher detection probability for European smelt. On the other hand eDNA metabarcoding can provide information on other species in the fish community which can potentially lead to a deeper understanding of ecological interactions between species and might be informative for management decision.