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The skin, gills, and gut are the most extensively studied mucosal organs in fish. These mucosal structures provide the intimate interface between the internal and external milieus and serve as the indispensable first line of defense. They have highly diverse physiological functions. Their role in defense can be highlighted in three shared similarities: their microanatomical structures that serve as the physical barrier and hold the immune cells and the effector molecules; the mucus layer, also a physical barrier, contains an array of potent bioactive molecules; and the resident microbiota. Mucosal surfaces are responsive and plastic to the different changes in the aquatic environment. The direct interaction of the mucosa with the environment offers some important information on both the physiological status of the host and the conditions of the aquatic environment. Increasing attention has been directed to these features in the last year, particularly on how to improve the overall health of the fish through manipulation of mucosal functions and on how the changes in the mucosa, in response to varying environmental factors, can be harnessed to improve husbandry. In this short review, we highlight the current knowledge on how mucosal surfaces respond to various environmental factors relevant to aquaculture and how they may be exploited in fostering sustainable fish farming practices, especially in controlled aquaculture environments.

The innate immune system of fish has conventionally been considered incapable of immunological memory, but is now being recognised as exhibiting memory-like features known as trained immunity. This study investigated the induction of trained immunity in Atlantic salmon ( Salmo salar L.) by training head kidney-derived leukocytes using β-glucan, followed by a resting phase and secondary stimulation with β-glucan (homologous) or lipopolysaccharide (LPS, heterologous). The cellular responses, metabolite production, and gene expression related to innate immunity, metabolism, and epigenetic markers were assessed. The effects of initial β-glucan training persisted after a 5-day resting period, during which upregulation occurred in the expression of key innate immune and metabolic genes. Upon secondary stimulation, leukocytes exhibited stimulus-dependent transcriptional responses with increased expression of several pro-inflammatory and metabolic genes, particularly in the heterologous LPS-exposed group. Attenuation of specific inflammatory cytokine responses occurred in trained cells upon LPS stimulation, but metabolic gene expression patterns indicated regulation toward enhancing glycolytic activity and mitochondrial oxidative metabolism. Trained cells also displayed significantly increased phagocytic activity, especially after heterologous exposure. Only minor or moderate changes occurred in other cellular outputs (reactive oxygen species, nitric oxide, lactate, and fumarate). Epigenetic markers showed limited expression changes. The experimental evidence indicates a phenotype similar to trained immunity in salmon leukocytes, characterised by transcriptional and functional alterations following β-glucan training; however, responses vary upon secondary exposure to a heterologous stimulus. This study provides new insight into trained immunity in Atlantic salmon by demonstrating the transcriptional and cellular response of leukocytes to develop stimulus-dependent immune and metabolic regulations.

The classical notion of a centralized clock that governs circadian rhythmicity has been challenged with the discovery of peripheral oscillators that enable organisms to cope with daily changes in their environment. The present study aimed to identify the molecular clock components in Atlantic cod (Gadus morhua) and to investigate their daily gene expression in fast skeletal muscle. Atlantic cod clock genes were closely related to their orthologs in teleosts and tetrapods. Synteny was conserved to varying degrees in the majority of the 18 clock genes examined. In particular, aryl hydrocarbon receptor nuclear translocator-like 2 (arntl2), RAR-related orphan receptor A (rora) and timeless (tim) displayed high degrees of conservation. Expression profiling during the early ontogenesis revealed that some transcripts were maternally transferred, namely arntl2,cryptochrome 1b and 2 (cry1b and cry2), and period 2a and 2b(per2a and per2b). Most clock genes were ubiquitously expressed in various tissues, suggesting the possible existence of multiple peripheral clock systems in Atlantic cod. In particular, they were all detected in fast skeletal muscle, with the exception of neuronal PAS (Per-Arnt-Single-minded)domain-containing protein (npas1) and rora. Rhythmicity analysis revealed 8 clock genes with daily rhythmic expression, namely arntl2, circadian locomotor output cycles kaput (clock), npas2, cry2, cry3 per2a, nuclear receptor subfamily 1, group D, member 1 (nr1d1), and nr1d2a. Transcript levels of the myogenic genes myogenic factor 5 (myf5) and muscleblind-like 1(mbnl1) strongly correlated with clock gene expression. This is the first study to unravel the molecular components of peripheral clocks in Atlantic cod. Taken together, our data suggest that the putative clock system in fast skeletal muscle of Atlantic cod has regulatory implications on muscle physiology, particularly in the expression of genes related to myogenesis.

The diplomonad parasite Spironucleus salmonicida causes spironucleosis, a systemic infection characterised by internal haemorrhaging, splenomegaly, and granulomatous lesions in multiple organs. Prevention is the primary control strategy, particularly in recirculating aquaculture systems (RAS). This study evaluated the effectiveness of common water-disinfection methods against the parasite. In situ experiments assessed parasite survival following exposure to low- and medium-pressure ultraviolet (UV) radiation at different doses. A subsequent in vivo trial simulated a biosecurity breach in RAS using Atlantic salmon smolts. Two loop-disinfection strategies were tested: continuous UV treatment (70–80 mJ/cm²) and ozone (300–350 mV oxidation–reduction potential), alongside a no-disinfection control. The parasite was introduced via make-up water over three days, and fish were monitored for four weeks. In situ, medium‑pressure UV doses ≥ 50 mJ/cm² immediately inactivated the parasite, whereas lower doses achieved inactivation within 48 h. In vivo, no fish developed disease, and the parasite was not detected in any group. Disinfection did not affect mucosal integrity, although ozone increased expression of oxidative stress markers in the gills. UV and ozone also altered microbial community composition. Overall, S. salmonicida was sensitive to medium-pressure UV, and under the tested conditions did not persist or cause disease in RAS.

Transcriptomics provides valuable data for functional annotations of genes, the discovery of biomarkers, and quantitative assessment of responses to challenges. Meta-analysis of Nofima’s Atlantic salmon microarray database was performed for the selection of genes that have shown strong and reproducible expression changes. Using data from 127 experiments including 6440 microarrays, four transcription modules (TM) were identified with a total of 902 annotated genes: 161 virus responsive genes – VRG (activated with five viruses and poly I:C), genes that responded to three pathogenic bacteria (523 up and 33 down-regulated genes), inflammation not caused by infections – wounds, melanized foci in skeletal muscle and exposure to PAMP (180 up and 72 down-regulated genes), and stress by exercise, crowding and cortisol implants (33 genes). To assist the selection of gene markers, genes in each TM were ranked according to the scale of expression changes. In terms of functional annotations, association with diseases and stress was unknown or not reflected in public databases for a large part of genes, including several genes with the highest ranks. A set of multifunctional genes was discovered. Cholesterol 25-hydroxylase was present in all TM and 22 genes, including most differentially expressed matrix metalloproteinases 9 and 13 were assigned to three TMs. The meta-analysis has improved understanding of the defense strategies in Atlantic salmon. VRG have demonstrated equal or similar responses to RNA (SAV, IPNV, PRV, and ISAV), and DNA (gill pox) viruses, injection of bacterial DNA (plasmid) and exposure of cells to PAMP (CpG and gardiquimod) and relatively low sensitivity to inflammation and bacteria. Genes of the highest rank show preferential expression in erythrocytes. This group includes multigene families (gig and several trim families) and many paralogs. Of pathogen recognition receptors, only RNA helicases have shown strong expression changes. Most VRG (82%) are effectors with a preponderance of ubiquitin-related genes, GTPases, and genes of nucleotide metabolism. Many VRG have unknown roles. The identification of TMs makes possible quantification of responses and assessment of their interactions. Based on this, we are able to separate pathogen-specific responses from general inflammation and stress.

Although it is well known that the biological and physical characteristics of skin mucus in fishes are strongly affected by changes in environmental conditions, the influence of photoperiod and time-dependent bacterial endotoxin stimulation is not well documented. In the present study, we determined the diel variations in the basal activities of secretory proteins with known defense functions in the skin mucus of Nile tilapia (Oreochromis niloticus) maintained under two photic environments: equal length of day and night (12L:12D, LD) or total darkness (0L:24D, DD). A second experiment was conducted to determine how time-dependent (i.e., day versus night) lipopolysaccharide (LPS) challenge could influence these skin mucosal defenses. The results revealed that LD signal differentially modulated the activities of mucosal immune molecules. Fish subjected to LD regime showed significantly higher levels of skin mucus lysozyme and protease at nighttime than at daytime. This distinct feature was not observed in fish under DD. There was no general mucosal response patterns to time-dependent LPS challenge. Nonetheless, protease and lysozyme, which were identified to be at elevated levels at night, were significantly modulated when the endotoxin was administered at nighttime. Ceruloplasmin was the only molecule that responded to LPS challenge at daytime, where its activity significantly increased at 8 h post-stimulation. Collectively, the results revealed that photoperiod cues influenced the activities of mucosal defenses and this may play, at least in part, in the temporal sensitivity to bacterial endotoxin.

Nitrifying biofilters oxidize harmful ammonia excreted by fish into less toxic nitrate within recirculating aquaculture systems (RAS). Biofilter performance and resulting RAS water quality largely depend on a robust microbiome that effectively converts nitrogenous wastes; however, occasional use of water disinfectants may also be necessary to reduce or eliminate specific fish pathogens. Disinfectants and sanitizers such as peracetic acid (PAA) work by disrupting microbial activity and could unintentionally alter the microbially-driven nitrification biofiltration process if allowed to circulate within an RAS. Furthermore, the target concentration and application method of PAA may influence the level of biofilter disruption. For this study, 12 replicated experimental-scale fluidized sand biofilters were dosed with PAA to achieve target concentrations ranging from 1.0-–2.5 mg/L, a typical low-dose treatment range to reduce or eliminate opportunistic pathogens. Two application methods were compared, including (i) a single pulse of PAA added every other day for five days, and (ii) smaller doses of PAA added every five minutes over four hours. The PAA decay was monitored and predosing and postdosing water quality parameters were assessed. Regardless of the target concentration or application method, PAA addition within the tested range did not cause significant disruption to the biofilters’ nitrification processes. This research demonstrates that PAA may be a viable water sanitizer for the RAS industry, although further research to refine safe application protocols is necessary.

Treatment development for parasitic infestation is often limited to disease resolution as an endpoint response, and physiological and immunological consequences are not thoroughly considered. Here, we report the impact of exposing Atlantic salmon affected with amoebic gill disease (AGD) to peracetic acid (PAA), an oxidative chemotherapeutic. AGD-affected fish were treated with PAA either by exposing them to 5 ppm for 30 min or 10 ppm for 15 min. Unexposed fish from both infected and uninfected groups were also included. Samples for molecular, biochemical, and histological evaluations were collected at 24 h, 2 weeks, and 4 weeks post-treatment. Behavioral changes were observed during PAA exposure, and post-treatment mortality was higher in the infected and PAA treated groups, especially in 10 ppm for 15 min. Plasma indicators showed that liver health was affected by AGD, though PAA treatment did not exacerbate the infection-related changes. Transcriptome profiling in the gills showed significant changes, triggered by AGD and PAA treatments, and the effects of PAA were more notable 24 h after treatment. Genes related to immune pathways of B- and T- cells and protein synthesis and metabolism were downregulated, where the magnitude was more remarkable in 10 ppm for 15 min group. Even though treatment did not fully resolve the pathologies associated with AGD, 5 ppm for 30 min group showed lower parasite load at 4 weeks post-treatment. Mucous cell parameters (i.e., size and density) increased within 24 h post-treatment and were significantly higher at termination, especially in AGD-affected fish, with some treatment effects influenced by the dose of PAA. Infection and treatments resulted in oxidative stress—in the early phase in the gill mucosa, while systemic reactive oxygen species (ROS) dysregulation was evident at the later stage. Infected fish responded to elevated circulating ROS by increasing antioxidant production. Exposing the fish to a crowding stress revealed the interference in the post-stress responses. Lower cortisol response was displayed by AGD-affected groups. Collectively, the study established that PAA, within the evaluated treatment protocols, could not provide a convincing treatment resolution and, thus, requires further optimization. Nonetheless, PAA treatment altered the mucosal immune and stress responses of AGD-affected Atlantic salmon, shedding light on the host-parasite-treatment interactions.

Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C. Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry. Results showed that high temperature had a stronger effect on the barrier functions of skin than the infection. Increased temperature induced gene expression changes in skin and spleen, heat shock protein 47 and cold inducible RNA binding protein were identified as potential gene markers for thermal stress. The effect of bacterial challenge was small at 12°C. At high temperature, the development of severe pathology in spleen coincided with a significant decrease of immunoglobulins transcripts, which contrasted with the activation of multiple immune genes. In addition, we used an in vitro model of skin biopsies and scale explants exposed to hydrogen peroxide (H2O2) to assess the effects of thermal and oxidative stress. High temperature and H2O2 reduced proliferation and migration of keratocytes, and increased expression of stress markers, and compounding effects were observed with combined stressors. Results suggest that the projected increased seawater temperature will pose a significant threat to Norwegian cod farming, affecting various biological processes and making fish more vulnerable to stressors and pathogens. Cod farming needs high attention to temperature changes, and special precautions should be taken if the temperature increases beyond cods’ thermal optimum.

A better understanding of recirculating aquaculture system (RAS) biosecurity is crucial for the sustainable and ethical production of Atlantic salmon smolt and post-smolt in these systems. This study described and evaluated the performance of a RAS facility for fish infection research with Atlantic salmon as the main animal model. Fish body weight, length, water quality, and system metrics from five independent experimental trials conducted between September 2020 and July 2021 were used to analyze the variation within and between treatments. Statistical power analysis was performed to determine the minimum number of fish required. The fish parameters variability showed that the inter-class correlation coefficient was on average low (0.1) and that the variation within tanks was larger than the variation between the tanks. The power analysis showed that 15 fish were required to be sampled per tank under these study conditions. Variation of water quality and system management metrics among the five experimental trials was higher compared to the variation within the five experimental trials. Moreover, the variation of the water quality parameters controlled by sensors was relatively low, whereas the parameters depending on biofilter maturation level and performance presented a very high variation. Water exchange rate-dependent quality parameters showed a similar variation value, i.e., nitrate and water turbidity. The established baseline for variability and performance presents an important reference for the design and realization of future experiments in RAS facilities. It is foreseen that the current research facility will develop new knowledge to improve the RAS biosecurity in the Atlantic salmon aquaculture industry.