Characterization of Bacterial Communities on Trout Skin and Eggs in Relation to Saprolegnia parasitica Infection Status

We have investigated the changes in the microbial communities on the surface of trout eggs and the skin of adult trout in relation to the presence of <i>Saprolegnia parasitica</i>. This pathogen causes saprolegniosis, a disease responsible for significant losses in salmonid farms and hatcheries. It is known from other disease systems that the host-associated microbiome plays a crucial role in the defence against pathogens, but if the pathogen predominates, this can lead to dysbiosis. However, analyses of the effects of <i>S. parasitica</i> on the diversity, composition, and function of microbial communities on fish skin and eggs are scarce. Thus, we have collected skin swabs from injured and healthy trout (<i>N</i> = 12), which differed in <i>S. parasitica</i> load, from three different fish farms in Croatia (Kostanjevac, Radovan, and Solin), while trout egg samples (<i>N</i> = 12) were infected with <i>S. parasitica</i> in the laboratory. Illumina sequencing of the V4 region of the <i>16S</i> rRNA marker gene showed that infection with <i>S. parasitica</i> reduced the microbial diversity on the surface of the eggs, as evidenced by decreased Pielou's evenness and Shannon's indices. We further determined whether the bacterial genera with a relative abundance of >5.0% in the egg/skin samples were present at significantly different abundances in relation to the presence of <i>S. parasitica</i>. The results have shown that some genera, such as <i>Pseudomonas</i> and <i>Flavobacterium</i>, decreased significantly in the presence of the pathogen on the egg surface. On the other hand, some bacterial taxa, such as <i>Acinetobacter</i> and <i>Janthinobacterium</i>, as well as <i>Aeromonas</i>, were more abundant on the diseased eggs and the injured trout skin, respectively. Finally, beta diversity analyses (weighted UniFrac, unweighted UniFrac, Bray-Curtis) have shown that the sampling location (i.e., fish farm), along with <i>S. parasitica</i> infection status, also has a significant influence on the microbial communities' composition on the trout skin and eggs, demonstrating the strong influence of the environment on the shaping of the host surface microbiome. Overall, we have shown that the presence of <i>S. parasitica</i> was associated with changes in the diversity and structure of the trout skin/egg microbiome. The results obtained could support the development of new strategies for the management of saprolegniosis in aquaculture.