NECR503 eDNA monitoring of restoration effects on the River Severn (Phase II) Unlocking the Severn LIFE project (NECR503)
Authors: Andreou, D., Griffiths, N., Hanfling, B., Sellers, G., Morissey, B., Svoboda, D. and Whatley, L.
Publisher: Natural England
Abstract:The ‘Unlocking the Severn’ project has reconnected 158 miles of shad and sea lamprey habitat through the creation of fish passes at four weirs on the River Severn between Diglis and Lincomb. Reconnection schemes in river systems can lead to changes in the fish community (Magilligan et al. 2016), therefore monitoring community composition and distribution of fishes prior and post reconnection is required to assess the impact of such changes. The aim of this project was to generate biodiversity data for 2022 using eDNA metabarcoding approaches which can be used to investigate wider ecological effects of restoring river connectivity in the River Severn (Unlocking the Severn LIFE project).
Specifically, we wished to map the distribution of shad (Alosa spp.) eDNA in relation to weirs in the Severn and investigate the possible presence of shad in the Thames; provide semi-quantitative data on fish community structure in the Severn and Thames; and compare the 2022 fish community data with data from previous metabarcoding surveys in 2021 and 2018 in the River Severn; and provide data on invertebrate diversity and community composition in the Severn and Thames respectively.
eDNA samples were collected at five sites in the River Severn and two sites in the river Thames, by Natural England (NE) and Canal and Rivers Trust (CRT) staff, with the help of CRT volunteers. Samples were collected over two dates during the putative shad spawning season at the same locations along the River Severn (9th May, 31st May) and Thames (12th May, 1st June) respectively. Replicate samples (250-900 ml each) were collected from mid-river at each location and individually filtered on site using Sterivex filters. Filters were sent to the laboratory for DNA extraction and sequencing using PCR with two different primer sets; fish specific primers targeting the mitochondrial (mt) 12S region (MiFish, Miya et al. 2015, 2020) and invertebrate specific primers targeting a section of the generic mt COI barcoding region (Leese et al. 2021). During the process PCR products were tagged with an index unique to each sample and then sequenced on an Illumina MiSeq using v3. Raw sequencing data were analysed using a reproducible metabarcoding bioinformatic protocols established at UHI Inverness.
During the first sampling event on the 9th May two of the sites at the downstream end of the sampling range tested positive for Alosa eDNA indicating that the species had not passed the Holt fish pass at Holt Fleet Bridge weir at this stage in the migration. During the second sampling event on the 31st May shad eDNA was found at all five sites indicating that the species had successfully negotiated all four weirs. No shad eDNA was detected at either of the two sites in the river Thames (Figure 3) at any of the sampling dates. A total of 25 and 20 fish taxa and 86 and 40 invertebrate species were detected in eDNA samples from the rivers Severn and Thames respectively. As expected, fish and invertebrate community structures differed considerably between the Severn and Thames. Fish species detected in this survey in the River Severn were largely the same as those detected in the 2021 eDNA metabarcoding survey. Shad DNA was detected above the Lincomb weir during the 2022 shad spawning run indicating that the shad are accessing the reconnected habitat in their first spawning event following reconnection. The results of previous surveys in the River Severn support the usefulness of eDNA metabarcoding in Page 6 of 53 eDNA monitoring of restoration effects on the River Severn (Phase II) NECR503 monitoring changes in fish communities resulting for habitat restoration, and potentially more broadly to assess water quality through surveying invertebrate communities. It is recommended that a long-term monitoring programme is established with consistent spatio-temporal coverage to enable the effect of eDNA dispersal on spatial variation; research into incorporating hydraulic modelling approaches into lotic eDNA surveys to allow spatially more accurate predictions of species distributions; and review existing invertebrate eDNA specific metrics for the use in future monitoring of ecological status.
https://publications.naturalengland.org.uk/publication/4660715684888576
Source: Manual