Molecular identification and environmental DNA detection of gill lice ectoparasites associated with Brook Trout declines

Abstract

ObjectiveGill lice Salmincola spp. are among the most widely reported parasites of freshwater salmonids and have been associated with recent declines in native Brook Trout Salvelinus fontinalis populations. Effective gill lice surveillance is vital for salmonid conservation success, but current survey approaches are often inadequate or problematic. We developed an environmental DNA (eDNA)‐based approach to detect the gill louse Salmincola edwardsii and explored the viability of this approach as a management tool for rapid, large‐scale gill lice surveillance at Fort McCoy, Wisconsin, USA.MethodsReference sequences were generated from gill lice specimens collected at Fort McCoy to confirm their identify as S. edwardsii and used to design a quantitative polymerase chain reaction (qPCR) assay that targets S. edwardsii mitochondrial cytochrome c oxidase I (COI). Assay validation included in silico and in vitro sensitivity and nontarget specificity testing, and assay performance was validated in situ by sampling eDNA at sites characterized via electrofishing.ResultMolecular analysis of reference sequences confirmed S. edwardsii identity while also providing the first multi‐population assessment of genetic variation for North American Salmincola and the most taxonomically comprehensive molecular phylogeny of Lernaeopodidae to date. Salmincola edwardsii eDNA was detected at 14 of 38 sites, including 12 of 14 sites with known active infestations, with no evidence that the odds of detecting gill lice via electrofishing was greater than the odds of detections from eDNA analysis. Brook Trout presence was highly predictive of gill lice eDNA site occupancy, concordant with S. edwardsii being an obligate parasite of Salvelinus fishes. However, by expanding survey coverage via eDNA analysis, we were able to identify an isolated drainage with Brook Trout where S. edwardsii is apparently absent, confirming electrofishing observations.ConclusionThese results suggest that eDNA analysis is equivalent to electrofishing for detecting gill lice in terms of performance yet offers substantial gains in survey efficiency. Further, this study demonstrates how eDNA analysis can provide valuable intel for directing management efforts, especially when used to expand survey coverage and prioritize follow‐up conventional surveys to assess host–parasite abundance, demographics, and status.

Comparison of qPCR and metabarcoding for environmental DNA surveillance of a freshwater parasite

“…To assess the performance of metabarcoding compared to qPCR for gill lice eDNA detection, we used the same samples originally collected and analyzed by Katz et al (2023) (Schrader et al, 2012). Extracted DNA was then stored in a −20°C freezer for 3 months until downstream qPCR and metabarcoding analyses were completed.…”

“…Furthermore, internal parasite detections that require fish capture and assessment are often lethal, further stressing vulnerable host populations (Duval et al., 2021 ). To address these limitations, researchers and natural resource managers are increasingly turning to environmental DNA (eDNA) to detect freshwater parasites (Bass et al., 2015 ; Duval et al., 2021 ; Katz et al., 2023 ).…”

“…( 2015 , 2023 ) reviewed the applications of eDNA specifically for detecting parasites, highlighting its potential for effectively detecting parasites in natural systems and demonstrating that eDNA often outperformed conventional surveying methods. While eDNA has shown success in detecting freshwater parasites, the majority of studies have focused on single species identification using quantitative polymerase chain reaction (qPCR) based methods (Huver et al., 2015 ; Katz et al., 2023 ; Richey et al., 2018 ; Rusch et al., 2018 ; Sengupta et al., 2019 ; Sieber et al., 2020 ). This species‐specific approach has been valuable, but advancing technology has paved the way for whole community analysis through eDNA metabarcoding.…”

“…Analyzing these same samples from Katz et al. ( 2023 ) allow us to compare the sensitivities of qPCR and metabarcoding.…”

“…Here, we performed invertebrate eDNA metabarcoding on samples originally collected and analyzed for the development and validation of the S. edwardsii eDNA qPCR assay (Katz et al., 2023 ). By comparing metabarcoding detections with qPCR results, we directly assess the efficacy of eDNA metabarcoding for gill louse detection and determine how its performance compares with qPCR.…”