Analysis of bacterial microbiome associated with nylon and copper nets in an aquaculture context

Abstract Bacterial pathogens represent a huge challenge for aquaculture profitability and fish welfare, particularly since they can naturally occur in the water column and fish microbiomes, appear associated with biofouling or establish biofilms on tanks, gear and nets. Recently, several studies have shown how biofilms can become important pathogen reservoirs within fish farms, particularly since they confer protection from external stressors, such as antibiotics, and can potentially favor virulence. Copper nets are presently regarded as a good alternative to other traditional netting material, such as nylon, due to their high durability and low maintenance, and also due to the antimicrobial properties of copper. Here we compared the bacterial microbiomes associated with nylon and copper nets in an aquaculture context, using a metataxonomic approach through the high-throughput sequencing of the 16S rRNA V4 hypervariable region. Bacterial alpha-diversity associated with nylon was significantly higher than the associate with copper nets. Similarly, there was a significant effect of net type on bacterial beta-diversity. Additionally, among the most abundant bacteria colonizing copper nets there were taxa belonging to Tenacibaculum and Winogradskyella, which are both known to harbor potential fish pathogens. We thus highlight the importance of monitoring the composition of bacterial communities established in aquaculture gear, including in copper nets, with future studies evaluating whether they may serve as reservoirs for pathogenic bacterial strains.