Effect of a prophylactic treatment with chloramine-T on gill histology and microbiome of Atlantic salmon (Salmo salar) under commercial conditions

Abstract Chloramine-T (Cl-T) is a disinfectant and sanitizer widely applied to treat bacterial infections on the gill and skin of Atlantic salmon during freshwater culture. It is typically applied as static or flush treatments during periods of disease risk or in response to pathogen detection or gross disease signs. While the efficacy of CI-T to reduce specific bacterial pathogens has been demonstrated previously, its effect on the broader commensal microbial community is largely unknown. To address this knowledge gap, the present study examined the effects of a one-hour Cl-T treatment (nominal 15 mg L−1) on the skin and gill microbiome using a 16S rRNA based amplicon sequencing approach. Furthermore, the total bacterial load and histological changes in the gill were examined following CI-T treatment. Although, bacterial quantification on gills and water confirmed decreased bacterial load at 1 h, these loads returned to pre-treatment levels by 24 h. Microbial richness of bacterial communities on skin and gills varied at 1 h, and 13 d compared to 0 h. Contrary to the gills, microbial diversity on skin decreased after treatment. Gill histology showed subepithelial oedema at 24 h and increased number of lamellar mucous cells at 7 d compared with 0 h. This study reports the effects of commercially deployed Cl-T on two gill health indicators: bacterial microbiome composition and gill morphology in fresh water farmed Atlantic salmon.