Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Rusch, Johannes C.; Hansen, Haakon; Strand, David; Markussen, Turhan; Hytterød, Sigurd; Vrålstad, Trude

doi:10.1186/s13071-018-2916-3

Cited by 58 publications

(52 citation statements)

References 47 publications

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“…Correlation was tested on the first-order difference series of eDNA concentrations (C L ) from noble crayfish and A. astaci using spearman rank correlation. The statistical tests were run in the software RStudio v. 1.1.456 (RStudio team, 2016) using r v 3.5.1 (R Development Core Team, 2018).…”

Section: Statisticsmentioning

confidence: 99%

Monitoring a Norwegian freshwater crayfish tragedy: eDNA snapshots of invasion, infection and extinction

Strand

Johnsen

Rusch

et al. 2019

Journal of Applied Ecology

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1. The European noble crayfish Astacus astacus is threatened by crayfish plague caused by the oomycete Aphanomyces astaci, which is spread by the invasive North American crayfish (e.g. signal crayfish Pacifastacus leniusculus). Surveillance of crayfish plague status in Norway has traditionally relied on the monitoring survival of cage-held noble crayfish, a method of ethical concern. Additionally, trapping is used in crayfish population surveillance. Here, we test whether environmental DNA (eDNA) monitoring could provide a suitable alternative to the cage method, and a supplement to trapping.2. We took advantage of an emerging crayfish plague outbreak in a Norwegian watercourse following illegal introduction of disease-carrying signal crayfish, and initiated simultaneous eDNA monitoring and cage-based surveillance, supplemented with trapping. A total of 304 water samples were filtered from several sampling stations over a 4-year period. eDNA data (species-specific quantitative real-time PCR [qPCR]) for the presence of A. astaci, noble and signal crayfish within the water samples were compared to cage mortality and trapping. 3. This is the first study comparing eDNA monitoring and cage surveillance during a natural crayfish plague outbreak. We show that eDNA monitoring corresponds well with the biological status measured in terms of crayfish mortality and trapping results. eDNA analysis also reveals the presence of A. astaci in the water up to 2.5 weeks in advance of the cage method. Estimates of A. astaci and noble crayfish eDNA concentrations increased markedly during mortality and vanished quickly thereafter. eDNA provides a snapshot of the presence, absence or disappearance of crayfish regardless of season, and constitutes a valuable supplement to the trapping method that relies on season and legislation. 4. Synthesis and applications. Simultaneous eDNA monitoring of Aphanomyces astaci (crayfish plague) and relevant native and invasive freshwater crayfish species is well-suited for early warning of invasion or infection, risk assessments, habitat evaluation and surveillance regarding pathogen and invasive/native crayfish 1662 | Journal of Applied Ecology STRAND eT Al.

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Section: Statisticsmentioning

confidence: 99%

Monitoring a Norwegian freshwater crayfish tragedy: eDNA snapshots of invasion, infection and extinction

Strand

Johnsen

Rusch

et al. 2019

Journal of Applied Ecology

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“…Quantitative PCR (qPCR) and digital droplet (dd) PCR are currently the main methods used to detect eDNA of focal species (Baker, Steel, Nieukirk, & Klinck, 2018;Boothroyd, Mandrak, Fox, & Wilson, 2016;Carlsson et al, 2017;Dejean et al, 2011;Gargan et al, 2017;Rusch et al, 2018;Thomsen, Kielgast, Iversen, Møller, et al, 2012;Uthicke, Lamare, & Doyle, 2018). However, the need to cycle from 95°C to lower temperatures during the PCR process makes the adaptation of PCR-based techniques to a portable biosensor device challenging (Zhang & Xing, 2007).…”

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confidence: 99%

The application of CRISPR‐Cas for single species identification from environmental DNA

Williams

O’Grady

Ball

et al. 2019

Molecular Ecology Resources

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We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR‐based techniques to detect a given species from eDNA samples, posing a logistical challenge for on‐site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR‐Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof‐of‐concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 hr). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.

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“…Environmental DNA is a term that may be used to define the wide range of genetic material present in environmental samples, from extracellular DNA to whole organisms (Barnes & Turner, ), and its analysis may be particularly relevant to the detection of parasites that are genetically diverse but morphologically difficult to distinguish. The potential for this approach has been established as a surveillance tool for G. salaris (Rusch et al, ). However, the unambiguous identification of parasites for notifiable disease management still requires the recovery of specimens.…”

Section: Introductionmentioning

confidence: 99%

Development of a non‐lethal hydrogen peroxide treatment for surveillance of Gyrodactylus salaris on trout farms and its application to testing wild salmon populations

Thrush

Hill

Taylor

2019

Transbound Emerg Dis

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This study documents the development of a non‐lethal sampling method to recover gyrodactylid parasites from large numbers of fish that will underpin an improved surveillance strategy for Gyrodactylus salaris. A review of published literature identified over 80 compounds that have previously been tested against gyrodactylids or closely related parasite species. Five safe and relatively fast‐acting compounds were selected for testing to determine their efficiency in removing gyrodactylids from host fish in small‐scale aquaria trials using three‐spined stickleback infected with Gyrodactylus gasterostei as a model host–parasite system. The most effective compound was hydrogen peroxide; short‐duration exposure (3 min) achieved a parasite detection sensitivity of 80%–89%. The practicality of exposing farmed salmonids to hydrogen peroxide for G. salaris surveillance was tested in the field by conducting a parasite recovery trial using a brown trout stock endemically infected with G. truttae and G. derjavinoides and comparing this to the whole‐body examination procedure currently conducted by UK authorities. Significantly more parasites were recovered after exposing fish to hydrogen peroxide and filtering the treatment solution than by direct whole‐body examination of killed fish (mean: 225 vs. 138 parasites per fish). The gyrodactylid recovery rate of the two methods was 84.6% and 51.9%, respectively. A comparison of timings for the two methods indicated scope for significant time savings in adopting the chemical screening method. The study demonstrated that hydrogen peroxide bath treatment may be successfully applied to the surveillance of gyrodactylid parasites and established as a non‐lethal method for sampling farmed and wild fish. This approach has the potential to reduce resources required to collect and isolate parasites for diagnostic testing and improve the sensitivity and confidence of surveillance programmes designed to demonstrate freedom from disease, thus underpinning a robust and defensible surveillance strategy for G. salaris for the UK aquatic animal disease contingency plan.

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Catching the fish with the worm: a case study on eDNA detection of the monogenean parasite Gyrodactylus salaris and two of its hosts, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)

Cited by 58 publications

References 47 publications

Monitoring a Norwegian freshwater crayfish tragedy: eDNA snapshots of invasion, infection and extinction

Monitoring a Norwegian freshwater crayfish tragedy: eDNA snapshots of invasion, infection and extinction

The application of CRISPR‐Cas for single species identification from environmental DNA

Development of a non‐lethal hydrogen peroxide treatment for surveillance of Gyrodactylus salaris on trout farms and its application to testing wild salmon populations

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