Saprolegniales are a group of predominantly aquatic Oomycetes of great economic and ecological importance in aquaculture and natural ecosystems. It is therefore crucial to detect and characterize them rapidly and reliably in the environment. In the last few years, metabarcoding has emerged as a powerful tool for assessing ecosystem diversity, especially microbial communities. Here, we present a new metabarcoding protocol based on the specific amplification of saprolegnialean 5.8S rRNA gene and the variable region internal transcribed spacer 2 (ITS2) using newly designed primers. We evaluated the efficiency of these primers on a set of DNA extractions on both pure cultures and environmental samples (filtered water and sediment). We found a high diversity of Saprolegniales species, including potentially pathogenic in species of aquaculture importance, such as Aphanomyces astaci causing crayfish plague , Saprolegnia australis, Saprolegnia diclina and Saprolegnia parasitica that severely impact the salmon industry. Aphanomyces invadans , causing epizootic ulcerative syndrome for aquacultured fish especially in warm water areas, was possibly detected here first time in an environmental sample from Europe. Overall, our study demonstrates the efficiency of our metabarcoding protocol for assessing Saprolegniales diversity in aquaculture and environmental samples. This protocol could serve as a quick, sensitive and efficient tool for monitoring emerging diseases in aquatic ecosystems. • Detection of a wide spectrum of Saprolegniales in water samples • Aphanomyces invadans has been reported for the first time in Europe at low levels. • Virulent species like Saprolegnia spp. and Aphanomyces astaci are identified. • Enables rapid pathogen surveillance in aquaculture and natural ecosystems.
ElKhouri-Vidarte et al. (Sun,) studied this question.