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Aims To investigate the relationship between microbial community profiles and gill pathology during a production cycle of Atlantic salmon in two commercial hatcheries. Methods and Results Relationships between gill histology, environmental conditions, and microbiome were determined using high-throughput data, including 16S rDNA amplicon sequencing data, histopathology data, and water quality parameters. Hatchery A used riverine water and operated a mixed system of recirculation aquaculture system (RAS) and flowthrough. Hatchery B was used bore water and operated a RAS. Melanin deposits, hyperplastic, and inflammatory lesions were observed histologically in the gills. A higher prevalence of melanin deposits was detected and correlated to a change in beta diversity of bacterial communities in early time points (fingerling and parr stages). High abundance of Sphaerotilus sp. Pseudomonas sp. Nitrospira sp. Exiguobacterium sp. Deinococcus sp. and Comamonas sp. was correlated with a high prevalence of melanin in filaments. Bacterial diversity increased as the fish cohort transitioned from RAS to flowthrough in hatchery A. Conclusions Under commercial conditions, the commensal community of gill bacteria was related to melanin prevalence. [ABSTRACT FROM AUTHOR]

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. • A commercial Chloramine-T bath reshaped salmon gill and skin microbiome. • The bacterial load on gills was reduced, but treatment did not alter diversity. • Bacterial load and diversity on skin were altered following Chloramine-T application. • An acute irritation response was observed in gills of treated fish. [ABSTRACT FROM AUTHOR]