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 functional feeds could mitigate disease progression.

Research was conducted across aquaculture sites in Scotland and Tasmania, offering contrasting environments with lower (Scotland) and higher (Tasmania) seawater temperatures. 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 regions and evaluate the efficacy of functional feeds under contrasting seawater temperatures.

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 in Scotland. Salmon from a single hatchery were monitored through spring, summer, and autumn across three production sites. In autumn, fish were divided into functional and control diet groups for an eight-week trial. The functional diet was enriched with long-chain omega-3 fatty acids, marine-derived proteins, antioxidants, and vitamins, designed to support robustness and gill health. PGD 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, fish were fed functional or control diets for eight weeks and monitored for PGD, 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).

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.

The biomarker panel provides new insights into the mechanisms of gill disease and represents a promising tool for future diagnostic applications. 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.

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 time since seawater transfer was a stronger determinant of gill health than smolt origin, with immune activation and tissue remodelling processes driving much of the observed variation. Non-invasive sampling using RNA extracted from gill swabs were also tested, showing promise for detecting the more abundantly expressed biomarkers.

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.

In a subset of fish from the autumn trial, those fed the functional diet showed slightly lower PGD scores than controls, but no statistically significant differences were observed for amoebic gill disease (AGD) scores, PGD scores, or body weight (Figure 2).

Figure 2. Mean AGD score, PGD score, and body weight of fish fed control or functional diets during the autumn trial. Fish on the functional 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), or bodyweight (p = 0.11). Mean body weight was marginally higher in the control group.

Overall, the functional diet did not produce measurable improvements in gill health or growth, likely reflecting both the complexity of gill disease and the additional interventions required during the study, which may have masked potential dietary effects. These findings suggest that while single nutritional interventions may offer some support, integrated health management approaches are necessary to address gill pathologies effectively.

Importantly, microbiome diversity consistently declined as pathology worsened, reinforcing its role as an indicator of disease state. Initial validation of candidate biomarkers during AGD outbreaks across both Scotland and Tasmania confirmed their potential for early detection in diverse production contexts.

In Tasmania, biomarker robustness was further demonstrated under higher seawater temperatures. However, functional feeds provided only limited mitigation of gill health impacts in these warmer conditions. 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 among 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 and reduce the effectiveness of nutritional interventions.

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 detect 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. Although functional feeds showed only limited benefits, the ability to assess their performance using validated biomarkers is itself a valuable outcome, allowing producers to evaluate interventions under specific environmental conditions. 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. Equipping the aquaculture industry with tools for early detection, targeted intervention, and better understanding of environmental risks has enhanced both sustainability and fish welfare. The findings provide a pathway toward more adaptive management strategies that are essential as climate change continues to alter disease dynamics in marine environments.

Publications associated with 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