Please use this identifier to cite or link to this item:
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Temporal changes in skin and gill microbiomes of Atlantic salmon in a recirculating aquaculture system – Why do they matter?
Author(s): Lorgen-Ritchie, Marlene
Clarkson, Michael
Chalmers, Lynn
Taylor, John F
Migaud, Herve
Martin, Samuel A M
Keywords: Atlantic salmon
Recirculating aquaculture system (RAS)
Temporal dynamics
Issue Date: 15-Sep-2022
Date Deposited: 23-Jun-2022
Citation: Lorgen-Ritchie M, Clarkson M, Chalmers L, Taylor JF, Migaud H & Martin SAM (2022) Temporal changes in skin and gill microbiomes of Atlantic salmon in a recirculating aquaculture system – Why do they matter?. Aquaculture, 558, Art. No.: 738352.
Abstract: Mucosal surfaces are key components of teleost health, providing defence against opportunistic pathogens and other insults. Maintaining the integrity of mucosal surfaces and their associated microbial communities, especially the gill and skin that have large surface areas exposed to the environment is essential. Production of Atlantic salmon in land-based recirculating aquaculture systems (RAS) has increased significantly in recent years as it allows greater control over stability of the environment in which fish are reared, reduces water demand and minimises environmental impacts. However, little is known about the impact of the RAS environment upon the temporal dynamics of skin and gill mucosal microbiomes. In this study we examined microbial communities in gill mucus, skin mucus and rearing water throughout freshwater (FW) RAS production, and at 1-week and 4-weeks following transfer to seawater (SW) in open cage production using 16S rRNA sequencing. Microbial diversity and richness in skin and gill mucus of fish reared in a RAS system were temporally dynamic. Dynamics in richness and diversity were similar in the two mucosal tissues, and to some extent also mirrored that of the surrounding water. Dysbiosis indicated by an abrupt decline in diversity during FW production coincided with an increase in the relative abundance of two taxa belonging to the RAS-biofilter-associated nitrogen-cycling genus Hydrogenophaga in RAS tank water and this was also observed in gill and skin mucus. Extensive overlap in core taxa was observed between gill and skin mucus, but host-specific cores were non-existent during the dysbiotic event with all cores present in the rearing water. Diversity remained stable during the transition from FW to SW, but distinct community composition and core taxa were observed in the two environments. Although RAS are closely controlled, significant temporal variation could be observed in temperature as well as levels of CO2 and nitrogen compounds, reflecting the increasing biological load within the system over time. The results presented here suggest that, in terms of microbiomes, dysbiosis may occur in both the RAS environment and fish mucosal surfaces over time, but microbial communities have the capability to recover.
DOI Link: 10.1016/j.aquaculture.2022.738352
Rights: This is an open access article distributed under the terms of the Creative Commons CC-BY license (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. You are not required to obtain permission to reuse this article.
Licence URL(s):

Files in This Item:
File Description SizeFormat 
1-s2.0-S0044848622004689-main.pdfFulltext - Published Version5.59 MBAdobe PDFView/Open

This item is protected by original copyright

A file in this item is licensed under a Creative Commons License Creative Commons

Items in the Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

The metadata of the records in the Repository are available under the CC0 public domain dedication: No Rights Reserved

If you believe that any material held in STORRE infringes copyright, please contact providing details and we will remove the Work from public display in STORRE and investigate your claim.