Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon

Birlanga, V. B., McCormack, G., Ijaz, U. Z. , MacCarthy, E., Smith, C. and Collins, G. (2022) Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon. Scientific Reports, 12, 16719. (doi: 10.1038/s41598-022-17008-2) (PMID:36202859) (PMCID:PMC9537138)

Abstract

Amoebic gill disease (AGD) and complex gill disease (CGD) are recurrent gill disorders in Atlantic salmon, resulting in significant aquaculture losses. The role of gill microbiomes in gill disease development is unclear. We undertook a longitudinal study to characterise the gill tissue and gill mucus microbiomes of farmed Atlantic salmon before, and during, a gill disease episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from microbiomes of gill samples taken from 105 individual salmon on a farm, over a summer season. The AGD aetiological agent, Neoparamoeba perurans, was PCR-quantified targeting 18S rRNA genes. Similar analyses were carried out on mucus samples. Mucus scrapings were suitable, non-lethal substitutes for characterisation of the gill prokaryotic community in this study. Gill tissue and gill mucus microbiomes changed during the campaign, correlating with N. perurans concentrations. Time explained 35% of the gill tissue and gill mucus microbiome variance, while N. perurans concentrations explained 5%. Genera including Dyadobacter, Shewanella and Pedobacter were maximally abundant in gill and mucus samples at the timepoint prior to the the detection of gill disorder signs, at T3. Shewanella was significantly more abundant before than during the gill disease episode, and we suggest this genus could be considered in future studies addressing relationships between gill disease and the gill microbiome.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Smith, Professor Cindy and Ijaz, Dr Umer
• Authors: Birlanga, V. B., McCormack, G., Ijaz, U. Z., MacCarthy, E., Smith, C., and Collins, G.
• College/School: College of Science and Engineering > School of Engineering > Infrastructure and Environment
• Journal Name: Scientific Reports
• Publisher: Nature Research
• ISSN: 2045-2322
• ISSN (Online): 2045-2322
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Scientific Reports 12: 16719
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
170256		Understanding microbial community through in situ environmental 'omic data synthesis	Umer Zeeshan Ijaz	Natural Environment Research Council (NERC)	NE/L011956/1	ENG - Infrastructure & Environment