Nanopore sequencing evidenced the presence of fish bacterial pathogens in the sea louse (Caligus rogercresseyi) microbiota collected from distant salmon farms in Chile

The recognized negative impacts of the ectoparasite Caligus rogercresseyi in the Chilean salmon aquaculture are primarily related to environmental and economic issues. However, recent evidence suggests a large and diverse microbial community associated with sea lice, where fish bacteria pathogens emerge as a sanitary concern. This study aimed to characterize the bacterial community associated with C. rogercresseyi, focusing on those microorganisms with potential impacts in salmon welfare. The sea lice-associated microbiota was identified using the microbial full-length16S rRNA gene sequencing by Oxford Nanopore Technology. Sea lice specimens were collected from three salmon farming zones in Los Lagos, Aysén, and Magallanes, Southern Chile. The bioinformatic analyses revealed DNA from potential pathogens inhabiting the C. rogercresseyi microbiota, representing 7.86% of the annotated sequences. Among the sampled sites, the most significant number of pathogenic bacteria DNA was found in Los Lagos (up to 23,6%), followed by Aysen (1,8%) and Magallanes (0.3%). Herein, genetic evidence from a total of 30 potential fish bacterial pathogens species were identified. Notably, fourteen Vibrio spp. were predominantly found in the Los Lagos region, while six Tenacibaculum spp. were more equally distributed among the sites. A core of five fish pathogens was observed in all farming zones, including Aliivibrio wodanis, Tenacibaculum dicentrarchi, Tenacibaculum ovolyticum, Tenacibaculum soleae, and Vibrio splendidus. Based on the reported findings, sea lice emerge as a potential reservoir for fish diseases in the aquatic environment. •30 Potential bacterial pathogens were identified in sea lice microbiota.•Vibrio spp. were predominantly found in the Los Lagos region.•Tenacibaculum spp. were more equally distributed among the sites.•sea lice emerge as a reservoir for fish diseases in the salmon industry.