Comparison of two water sampling approaches for eDNA-based crayfish plague detection

The crayfish plague agent Aphanomyces astaci causes high fatality rates among European crayfish species and is transmitted by semi-immune North American crayfish species via zoospores. Recently environmental DNA (eDNA) techniques have been developed to detect the pathogen directly in water samples. To identify the optimal technique for concentrating spores out of water samples we tested two water filtration methods, namely depth filtration (DF) and dead-end ultrafiltration (DEUF), with subsequent qPCR-based detection of A. astaci spores from the water column in three river systems in Germany. Both eDNA methods were successful in recovering and detecting A. astaci spores from all three lotic water systems and the detection patterns were generally consistent across watercourse and season. Water turbidity negatively affected the A. astaci spore detection with both eDNA methods, with increasing pellet weights for the DEUF method and decreasing water volumes for the DF samples. Although filtering high-volume water samples with the DEUF method led to slightly higher detection rates of A. astaci and seemed to be more sensitive in A. astaci detection, its application is highly laborious and more costly. We therefore propose to use the DF method for large-scale screenings of A. astaci in running waters due to its fast, cost-effective and easy-to-apply sample processing and the very robust quantification results. We are confident that this method might be favored as well for eDNA studies of other organisms.