Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity. One significant problem is the sea louse, which is controlled using pesticide treatments; however, the emergence of delousing drug resistance has been reported. Strategies based on salmon breeding selection represent a sustainable alternative for producing fish resistant to sea lice infestation. The effects of resistant and susceptible salmon phenotypes on the sea louse population must be better evaluated.
This study reported the sea lice microbiome and transcriptome signatures infecting different salmon phenotypes. Sea lice were collected from salmon families designated as resistant (R) and susceptible (S) after three successive infestations. RNA-Seq analysis and microbiome assessments were performed on sea lice using NovaSeq (Illumina) and MinION (Nanopore) platforms, respectively.
Differences in transcriptome expression patterns were observed between sea lice obtained from different salmon phenotypes. Sea lice from susceptible salmon showed a high number of genes up-regulated associated with metabolic processes; however, sea lice obtained from the resistant phenotype exhibited up-regulation of genes associated with stimulus response and biological regulation. Furthermore, sea lice obtained from the susceptible salmon showed high bacterial diversity. Interestingly, the bacterial genera Tenacibaculum and Pseudomonas were identified in the sea lice coming from the susceptible salmon family. Our results enhance the understanding of the sea lice infestation mechanism by incorporating the microbiome and transcriptome modulation study, which could be used to improve sea lice control strategies.