Environmental DNA detection of Arctic char (Salvelinus alpinus) in Irish lakes: Development and application of a species‐specific molecular assay

Abstract

Populations of Arctic char (Salvelinus alpinus) inhabiting Irish lakes are undergoing a rapid decline. In order to aid monitoring of this species in Irish lakes, a species‐specific qPCR assay was designed and subsequently tested for the detection of Arctic char's environmental DNA (eDNA) in an indoor mesocosm and in natural habitats (six lakes). Specifically, the mesocosm experiment revealed that sample volume can have significant effects on the application of eDNA approaches, whereby probability of detection depends from proximity to the source organism and volume of water filtered. When tested in the wild, positive amplification of Arctic char eDNA was observed in four of the six lakes sampled, proving that this approach can be successfully implemented in natural conditions. However, findings from the present study also showed that suboptimal sampling strategies can lead to false‐negative results (e.g., failure to detect the species when it is present). This study corroborates findings from other research on eDNA detection of fish species, showing that despite its current limitations, this approach can be a fast, noninvasive, and effective tool in aid to the conservation and management of freshwater fish species.

Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle

“…The forward and reverse primer sequences were removed, allowing three mismatches in the primer. Low-quality bases were removed by trimming the reads at the beginning of the first poor quality window, and defined as a 10 bp region with an average quality score less than 25 (Mirimin et al 2020). Reads meeting these criteria were further filtered to retain those with a length between the 140 bp minimum and 313 bp maximum.…”

Environmental DNA Based Surveillance for the Highly Invasive Carpet Sea Squirt Didemnum vexillum: A Targeted Single-Species Approach

“…In addition to the specificity of the eDNA assay, clear definitions of the limit of detection (LOD) and quantification (LOQ) are essential to generate robust and accurate data. Different templates are used to generate the LOD and LOQ calibration plots with either target species genomic DNA (Gillum et al, 2014;Miralles et al, 2016Miralles et al, , 2019Mauvisseau et al, 2019;LeBlanc et al, 2020), synthetic DNA constructs (Larson et al, 2017;Harper et al, 2018;Mirimin et al, 2019;Roux et al, 2020), or a PCR product of the target gene (Wood et al, 2019) being commonly utilized. The standards in calculating and reporting these parameters continue to vary widely in the published literature and consequently the LOD and LOQ are reported either as a copy number or concentration of a given target per reaction or microliter.…”

Development and field validation of RPA‐CRISPR‐Cas environmental DNA assays for the detection of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus)

“…Unfortunately, this isolation of Arctic char populations makes them highly vulnerable to climatic changes particularly in the southerly part of their distribution (Connor et al, 2019). Anthropogenic pressures such as agricultural intensification (Igoe et al, 2001), eutrophication, acidification, aquaculture and introduction of nonindigenous species are causing a rapid decline in populations, with 30% of Irish populations now considered extinct (Mirimin et al, 2020). These increasing threats make it vital for Arctic char to be monitored and protected, such as dictated in the European Water Framework Directive, to prevent further decline (Mirimin et al, 2020).…”

“…The primary objective of this study was to further demonstrate the utility of RPA‐CRISPR‐Cas assays for single taxa detection by extending its application to two additional species i.e., brown trout and Arctic char. These assays offer an alternative approach to the PCR‐based methods previously developed (Capo et al, 2019; Minett et al, 2021; Mirimin et al, 2020; Rodgers et al, 2018). As a highly specific isothermal assay that works at 37°C, RPA‐CRISPR‐Cas assays offer significant potential for cost effective on‐site biosensing applications and they may also be more robust in the presence of PCR inhibitors and challenging eDNA sample types such as those derived from sediment.…”

“…Arctic char is a cold water salmonid found throughout the Northern Hemisphere. Whilst often considered an anadromous species, in Ireland, populations have fully adapted to a freshwater life cycle (Mirimin et al, 2020). Due to confinement at the end of the last ice age (Maitland et al, 2007), populations are highly isolated from each other across Ireland and Great Britain, leading to large genetic variation previously recognized as distinct species (Maitland et al, 2007).…”