Unlocking gill health: biomarkers and management of disease in farmed Atlantic salmon

BACKGROUND

Gill health is critical to fish welfare and the efficiency of aquaculture production, yet it is highly vulnerable to pathogens and environmental stressors, particularly as ocean conditions change. This project investigated the drivers of complex gill disease (CGD) in farmed Atlantic salmon, identified molecular biomarkers and microbial signatures of gill health, and evaluated whether a nutritional strategy could mitigate disease progression.

Research was conducted across aquaculture sites in Scotland and Tasmania (2019-2021), offering the opportunity to study gill health in contrasting environments. A multi-disciplinary approach combined RNA sequencing (RNA-seq), histopathology, microbiota profiling, and high-throughput qPCR validation, providing a detailed, multi-layered assessment of gill pathology and its relationship with environmental drivers.

AIMS

The project set out to:

1. Identify the spatial and temporal drivers of gill pathology.
2. Examine the relationship between gross proliferative gill disease (PGD) scores, gill histopathology and gill gene expression.
3. Develop a panel of gene biomarkers and microbial signatures to monitor gill health.
4. Assess the robustness of these biomarkers across project regions and evaluate the efficacy of an experimental functional feed under commercial conditions.

APPROACH AND WORK PACKAGES

The project was divided into four work packages, each addressing a specific objective.

Work Package 1 focused on spatial and temporal sampling across Scottish production sites. Salmon from a single hatchery were monitored through spring, summer, and autumn across three production sites (2021 input). In autumn, fish were divided into test feed and control diet groups for an eight-week trial at one selected site. The experimental diet was enriched with long-chain omega-3 fatty acids, marine-derived proteins, antioxidants, and vitamins, designed to support robustness and gill health. Gross PGD & AGD scores, histopathology, microbiota profiling, transcriptomics (RNA-seq), and environmental data were collected.

Work Package 2 focused on biomarker development. Gill swabs and tissues were analysed for microbial diversity, histological changes, and gene expression. RNA-seq and high-throughput qPCR on the BioMark X platform were used to identify differentially expressed genes linked to disease progression. Candidate gene biomarkers were then shared with industry stakeholders for evaluation.

Work Package 3 extended testing to Tasmania. Under warmer seawater conditions (2019-2020), fish were monitored for AGD, microbial composition, histopathology, and gene expression. This allowed validation of gene biomarkers across distinct environments and provided insights into the role of climate in shaping gill disease.

Work Package 4 emphasised knowledge transfer. Findings were disseminated via stakeholder websites, reports, peer-reviewed publications, conference presentations, and a dedicated SAIC workshop.

RESULTS

The project delivered a comprehensive understanding of the biological and environmental drivers of gill disease in farmed Atlantic salmon. A major outcome was the development of a robust panel of more than 90 gene biomarkers associated with gill health, identified through RNA sequencing and validated using high-throughput qPCR (Figure 1). Through the currently funded SAIC Aqua Gill project, this panel of genes will be further developed towards commercial application.  

Figure 1. Correlation between RNA-seq transcript abundance (TPM) and high-throughput qPCR expression values for four candidate biomarkers (CLEC4M, IL1B, ALOXE3, and MMP17). Strong positive correlations confirm reproducibility across platforms, particularly for highly expressed genes, and informed the refinement of the final biomarker panel.

Many of the validated genes were common to salmon from both Scotland and Tasmania, while others location-specific (Table 1).

Table 1. Origin and classification of validated gene markers.

In parallel, the study identified distinct microbial signatures associated with gill disease progression, with taxa such as Candidatus Branchiomonas, Candidatus Rubidus, and Tenacibaculum consistently linked to pathology. The biomarker panel and microbial signatures provide new insights into the mechanisms of gill disease and represents a promising tool for future diagnostic and health interventions.

In Scotland, seasonal variation was a key factor, with gill disease peaking in autumn and correlating strongly with environmental conditions. Microbiome diversity declined significantly after transfer to seawater, at which point Candidatus Clavichlamydia salmonicola became dominant. Transcriptomic analysis showed that immune activation and tissue remodelling processes were driving much of the observed variation between samples. Non-invasive sampling using RNA extracted from gill swabs were tested, showing promise for detecting the more abundantly expressed biomarkers. In the future, using swabs to determine biomarker expression could add an important non-invasive tool to a health practitioner’s toolbox.

The evaluation of biomarkers across production sites highlighted a consistent relationship between microbial composition, histopathology, and gene expression patterns. Histological analysis confirmed progressive changes in gill tissue during disease development, while RNA-seq data revealed upregulation of genes involved in immune responses, inflammation, and pathogen defence. This validated the project aims by suggesting that integrated biomarkers could be used as surveillance tools.

Despite a good experimental design for the two test feeds included in this trial, diet codes were comparable for overall AGD and PGD score (Figure 2).  Due to the realities of working in a commercial situation, low realised gill scores across groups and scheduled interventions, dietary inference was not conclusive. The project highlights the need for innovation to allow for commercial scale assessment of management practises and their effect on fish resilience.  

Figure 2. Mean AGD score, PGD score of sampled fish fed control or test diet during the autumn trial. Fish on the test diet showed slightly lower average PGD scores than controls, but Mann-Whitney U tests indicated no statistically significant differences for AGD (p = 0.27), PGD (p = 0.40).

In Tasmania, biomarker robustness was further demonstrated under higher seawater temperatures. Pathogen communities differed notably between regions: while Scottish fish showed signatures of bacterial drivers, Tasmanian fish were heavily affected by Neoparamoeba perurans, the causative agent of AGD. Transcriptomic profiling identified inflammation-related genes as promising early-warning indicators in these outbreaks. Freshwater treatment, although commonly used to manage AGD, produced highly variable outcomes amongst individual fish, suggesting that more personalised or adaptive management strategies may be required. The findings also underscored the challenges posed by climate change, with rising ocean temperatures likely to intensify gill disease severity

The project’s dissemination and engagement activities ensured that findings reached both scientific and industry audiences. Results were communicated through peer-reviewed publications, conference presentations, stakeholder reports, and a dedicated SAIC workshop on gill health diagnostics. Project leaders also contributed expertise to a Scottish Parliamentary inquiry into salmon aquaculture, demonstrating the broader policy relevance of the research.

IMPACT

The project has made a significant contribution to the understanding and management of complex gill disease in salmon aquaculture. By integrating RNA-seq, histopathology, microbiota profiling, and qPCR validation, it delivered robust biomarkers and microbial indicators that can be applied in commercial settings for real-time disease monitoring. These tools lay the foundation for precision aquaculture, where fish health professionals and producers can identify problems earlier, refine management strategies, and adapt production models in response to environmental pressures.

One of the most important impacts lies in the ability to improve disease surveillance through molecular biomarkers, offering a step-change in diagnostic capability. Predictive gene signatures developed through this work provide a means to target interventions more effectively, whether through feed strategies, selective breeding, or tailored husbandry practices. The research also highlighted the importance of incorporating microbiome monitoring into disease management, particularly as climate-driven shifts in microbial communities are expected to play an increasing role in shaping gill health outcomes.

Beyond immediate applications, the project has generated intellectual and technical assets that strengthen the sector’s long-term resilience. The validated biomarker panel, alongside refined RNA-seq and qPCR methodologies, provides the foundation for future innovation in diagnostics. Training of research staff in advanced molecular and bioinformatic techniques has expanded expertise within the field, while adoption of high-throughput screening technologies has accelerated the potential for commercial implementation.

Knowledge transfer was another key achievement, with outputs widely disseminated through publications, workshops, and industry partnerships. These activities ensure that the findings are not confined to academic circles but actively shape operational practices. The project’s contribution to policy discussions further underscores its significance, positioning gill health as a central concern in the sustainable development of aquaculture.

Ultimately, the project bridges cutting-edge research with practical solutions. By providing the aquaculture industry with tools for early detection, and an insight into environmental risks, improvements to both fish welfare and production efficiency can be made.

Publications associated with this project:

Costelloe, EP, Lorgen-Ritchie, M, Król, E, Noguera, P, Bickerdike, R, Tinsley, J, Valdenegro, V, Douglas, A &  Martin, SAM. 2025, 'Microbial and histopathological insights into gill health of Atlantic salmon (Salmo salar) across Scottish aquaculture sites', Aquaculture, vol. 599, 742166. https://doi.org/10.1016/j.aquaculture.2025.742166

Vallarino, MC, Dagen, SL, Costelloe, E, Oyenekan, SI, Tinsley, J, Valdenegro, V, Król, E, Noguera, P & Martin, SAM 2024. 'Dynamics of Gill Responses to a Natural Infection with Neoparamoeba perurans in Farmed Tasmanian Atlantic Salmon', Animals, vol. 14, no. 16, 2356. https://doi.org/10.3390/ani14162356

Król, E, Noguera, P, Shaw, S, Costelloe, E, Gajardo, K, Valdenegro, V, Bickerdike, R, Douglas, A & Martin, SAM 2020. 'Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons from Multi-site Sampling', Frontiers in Genetics, vol. 11, 610. https://doi.org/10.3389/fgene.2020.00610