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Diseases of Aquatic Organisms

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DAO 141:171-184 (2020)  -  DOI: https://doi.org/10.3354/dao03524

Validation of an eDNA-based method for the detection of wildlife pathogens in water

Natalie Sieber1,2,*, Hanna Hartikainen1,2,3, Christoph Vorburger1,2

1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
2ETH Zürich, Institute of Integrative Biology (IBZ), 8092 Zürich, Switzerland
3University of Nottingham, School of Life Sciences, University Park, NG7 2RD, Nottingham, UK
*Corresponding author:

ABSTRACT: Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.


KEY WORDS: Aquatic parasites · Environmental DNA · Tetracapsuloides bryosalmonae · Batrachochytrium dendrobatidis · In situ filtration · Quantitative PCR


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Cite this article as: Sieber N, Hartikainen H, Vorburger C (2020) Validation of an eDNA-based method for the detection of wildlife pathogens in water. Dis Aquat Org 141:171-184. https://doi.org/10.3354/dao03524

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