Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.)

Abstract

Delousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.

Figure 1

Sex differences in broodstock Atlantic salmon skin microbial communities. (a) Mean Shannon diversity index of female and male Atlantic salmon skin microbial communities at time 0 pre-delousing (start of the experiment). (b) Mean Chao 1 index of female and male Atlantic salmon skin microbial communities at time 0 pre-delousing (start of the experiment). (c) Principal coordinate analysis of female and male broodstock Atlantic salmon skin microbial communities at time 0 pre- delousing. **** indicates a P-value < 0.0001 by t-test. Ellipses show significance at a confidence interval of 95% (P < 0.05).

Figure 2

Effects of mechanical delousing on the skin microbial community of female and male broodstock Atlantic salmon. Mean Shannon diversity index of female (a) Atlantic salmon and (b) male Atlantic salmon skin microbial communities at day 0 pre-delousing, day 0 post-delousing, 2 dpd and 13 dpd. Mean Chao-1 index of female (c) Atlantic salmon and (d) male Atlantic salmon skin microbial communities at day 0 pre-delousing, day 0 post-delousing, 2 dpd and 14 dpd. Principal component analysis of female (e) Atlantic salmon and (f) male Atlantic salmon skin microbial communities at day 0 pre-delousing, day 0 post-delousing, 2 dpd, and 13 dpd. Different letters designate statistically significant groups using one-way ANOVA followed by Sidak’s test for multiple comparisons with a P < 0.05. Ellipses show significance at a confidence interval of 95% (P < 0.05).

Figure 3

Delousing changes the bacterial community composition of the Atlantic salmon skin microbiome. (a) Relative abundance at the phylum level of the female and male skin microbial community composition at day 0 pre-delousing, day 0 post-delousing, 2 dpd and 13 dpd. (b) Relative abundance at the family level of the female (a) and male (b) skin microbial community composition at day 0 pre-delousing, day 0 post-delousing, 2 dpd and 13 dpd.

Figure 4

Significantly different ASVs in female and male Atlantic salmon skin microbial community day 0 post-delousing, 2 dpd and 13 dpd.

Figure 5

Delousing causes differential expansions of bacterial taxa in female and male skin microbial communities. Relative abundance of (a) Flavobacteriaceae, (b) Mycoplasmataceae, (c) Desulfovibrionaceae, (d) Shewanellaceae, (e) Pseudoalteromonadaceae (f) Pseudomonadaceae in female and male Atlantic salmon skin microbial communities at day 0 pre-delousing, day 0 post-delousing, 2 dpd and 13 dpd. P-values for Sidak’s multiple comparisons test are shown in the tables underneath each of the graphs.

Figure 6

The skin microbial community of female Atlantic salmon recovers quicker from delousing perturbance compared to males. Weighted UniFrac distance of the female skin microbial community compared to day 0 pre-delousing in females (a) and males (b). ***indicates a P-value < 0.001 and ****indicates a P-value < 0.0001 by t-test.

Figure 7

PICRUSt2 analysis of the skin microbial communities of female and male Atlantic salmon following delousing predicts sex-dependent altered biological pathways. (a) Predicted biological pathways significantly altered in the female Atlantic salmon skin microbial community day 0 post-delousing, 2 dpd and 13 dpd compared to day 0 pre-delousing. (b) Predicted biological pathways significantly altered in the male Atlantic salmon skin microbial community day 0 post-delousing, 2 dpd and 13 dpd compared to day 0 pre-delousing. For each sex only the top 10% of the significantly modified pathways are shown.

Figure 8

Schematic representation of the experimental set up and sampling for this study. The fish within a cage were constrained before pumping them (1) into the well boat (2) where they were allowed to settle for one hour before pumping (3) them through the Hydrolicer system. Fish exited into a collection tank (5) before they were pumped back into their respective cage (6). The fish were constrained in their respective cage before pumping them into a well boat. At time 0, day 2 and 13 post-delousing, fish were collected with a lift-up net from the cages straight into a tank (point 4). The fish collected for sampling into a tank (point 4) was transported to a land-based sampling facility (point 7), anesthetized in smaller buckets and sampled for skin from the same spot on the fish as shown in 8. Samples were collected at Time 0 before treatment, representing the fish in the cage post constraint, post treatment before they were pumped back to cages (5), and from point 6 at days 2 and 13 post treatment. Figure created with Biorender.