Atlantic Salmon Parr Research Articles

Acute stress response on Atlantic salmon: a time-course study of the effects on plasma metabolites, mucus cortisol levels, and head kidney transcriptome profile

Farmed Atlantic salmon (Salmo salar) welfare and performance can be strongly influenced by stress episodes caused by handling during farming practices. To better understand the changes occurring after an acute stress response, we exposed a group of Atlantic salmon parr to an acute stressor, which involved netting and transferring fish to several new holding tanks. We describe a time-course response to stress by sampling parr in groups before (T0) and 10, 20, 30, 45, 60, 120, 240, 300, and 330 min post-stress. A subgroup of fish was also subjected to the same stressor for a second time to assess their capacity to respond to the same challenge again within a short timeframe (ReStressed). Fish plasma was assessed for adrenocorticotropic hormone (ACTH), cortisol, and ions levels. Mucus cortisol levels were analyzed and compared with the plasma cortisol levels. At 5 selected time points (T0, 60, 90, 120, 240, and ReStressed), we compared the head kidney transcriptome profile of 10 fish per time point. The considerably delayed increase of ACTH in the plasma (60 min post-stress), and the earlier rise of cortisol levels (10 min post-stress), suggests that cortisol release could be triggered by more rapidly responding factors, such as the sympathetic system. This hypothesis may be supported by a high upregulation of several genes involved in synaptic triggering, observed both during the first and the second stress episodes. Furthermore, while the transcriptome profile showed few changes at 60 min post-stress, expression of genes in several immune-related pathways increased markedly with each successive time point, demonstrating the role of the immune system in fish coping capacity. Although many of the genes discussed in this paper are still poorly characterized, this study provides new insights regarding the mechanisms occurring during the stress response of salmon parr and may form the basis for a useful guideline on timing of sampling protocols.

Mapping key neuropeptides involved in the melanocortin system in Atlantic salmon (Salmo salar) brain.

The melanocortin system is a key regulator of appetite and food intake in vertebrates. This system includes the neuropeptides neuropeptide y (NPY), agouti-related peptide (AGRP), cocaine- and amphetamine-regulated transcript (CART), and pro-opiomelanocortin (POMC). An important center for appetite control in mammals is the hypothalamic arcuate nucleus, with neurons that coexpress either the orexigenic NPY/AGRP or the anorexigenic CART/POMC neuropeptides. In ray-finned fishes, such a center is less characterized. The Atlantic salmon (Salmo salar) has multiple genes of these neuropeptides due to whole-genome duplication events. To better understand the potential involvement of the melanocortin system in appetite and food intake control, we have mapped the mRNA expression of npy, agrp, cart, and pomc in the brain of Atlantic salmon parr using in situ hybridization. After identifying hypothalamic mRNA expression, we investigated the possible intracellular coexpression of npy/agrp and cart/pomc in the tuberal hypothalamus by fluorescent in situ hybridization. The results showed that the neuropeptides were widely distributed, especially in sensory and neuroendocrine brain regions. In the hypothalamic lateral tuberal nucleus, the putative homolog to the mammalian arcuate nucleus, npya, agrp1, cart2b, and pomca were predominantly localized in distinct neurons; however, some neurons coexpressed cart2b/pomca. This is the first demonstration of coexpression of cart2b/pomca in the tuberal hypothalamus of a teleost. Collectively, our data suggest that the lateral tuberal nucleus is the center for appetite control in salmon, similar to that of mammals. Extrahypothalamic brain regions might also be involved in regulating food intake, including the olfactory bulb, telencephalon, midbrain, and hindbrain.

Determination of the Oxidative Stress Biomarkers of 8-Hydroxydeoxyguanosine and Dityrosine in the Gills, Skin, Dorsal Fin, and Liver Tissue of Atlantic Salmon (Salmo salar) Parr.

Oxidative stress is a condition caused by an imbalance in the occurrence of reactive oxygen species in the cells and tissues of organisms. An ultra-performance liquid chromatography–electrospray ionization tandem mass spectrometry (UPLC–ESI–MS/MS) method was developed for the simultaneous determination of two oxidative stress biomarkers, 8-hydroxydeoxyguanosine (8OHDG) and dityrosine (DIY), in the gills, skin, dorsal fin, and liver tissue of Atlantic salmon (Salmo salar) parr. The use of target analyte-specific 13C and 15N internal standards allowed quantification of each target analyte to be performed through the standard solvent calibration curve. The relative recoveries [mean ± (relative standard deviation%)] of 8OHDG and DIY were 101 ± 11 and 104 ± 13% at a fortified concentration of 10 ng/mL (8OHDG) and 500 ng/mL (DIY), respectively, ensuring the accuracy of the extraction and quantification. The chromatographic separation was carried out using a gradient elution program with a total run time of 5 min. The limits of detection (LODs) were 0.11 and 1.37 ng/g wet weight (w.w.) for 8OHDG and DIY, respectively. To demonstrate the applicability of the developed method, it was applied in 907 tissue samples that were collected from Atlantic salmon parr individuals reared in an experimental land-based recirculating aquaculture system (RAS) treated with peracetic acid. Moreover, the possibility of using the dorsal fin as an alternative matrix for the minimally invasive assessment of oxidative stress in Atlantic salmon parr was introduced. To our knowledge, 8OHDG and DIY were used for the first time as biomarkers for biomonitoring the fish health (oxidative stress) of Atlantic salmon parr in RAS.

Experimental infection trials with European North Atlantic ranavirus (Iridoviridae) isolated from lumpfish (Cyclopterus lumpus, L.).

European North Atlantic ranavirus (ENARV, Iridoviridae), is a ranavirus species recently isolated from lumpfish (Cyclopterus lumpus, L.), which are used as cleaner fish in Atlantic salmon (Salmo salar) farming in Northern Europe. This study aimed to investigate (1) the virulence of ENARV isolates from Ireland, Iceland and the Faroe Islands to lumpfish; (2) horizontal transmission between lumpfish; and (3) virulence to Atlantic salmon parr. Lumpfish were challenged in a cohabitation model using intraperitoneally (IP) injected shedders, and naïve cohabitants. IP challenge with isolates from Iceland (1.9× 107 TCID50 ml-1 ) and the Faroe Islands (5.9× 107 TCID50 ml-1 ) reduced survival in lumpfish, associated with consistent pathological changes. IP challenge with the Irish strain (8.6× 105 TCID50 ml-1 ) did not significantly reduce survival in lumpfish, but the lower challenge titre complicated interpretation. Horizontal transmission occurred in all strains tested, but no clinical impact was demonstrated in cohabitants. Salmon parr were challenged by IP injection with the Irish isolate, no virulence or virus replication were demonstrated. A ranavirus qPCR assay, previously validated for fish ranaviruses, was first used to detect ENARV in tissues of both in lumpfish and Atlantic salmon. This study provides the first data on the assessment of virulence of ENARV isolates to lumpfish and salmon, guidelines for the diagnosis of ENARV infection, and poses a basis for further investigations into virulence markers.

In-water electric stunning as a humane commercial method for culling juvenile salmonids

Culling excess juvenile fish is a necessary and routine part of hatchery management. This is often achieved with an overdose of anaesthetic, which protects fish welfare at the time of killing. However, the use of anaesthetics means the resulting fish carcasses must be treated as controlled waste, which can be costly to dispose of. Electric stunning and killing of cull fish allows the carcasses to be sold as a protein source or disposed of as normal organic waste. For electric stunning and killing to protect welfare, unconsciousness should be achieved immediately and last until death. In this paper, we report on two trials investigating the efficacy of a commercial stunner designed for culling juvenile salmonids. To test whether unconsciousness was achieved immediately, Atlantic salmon smolts and fry in a small tank were exposed to an electric field similar to that inside the stunner for 1 s. Subsequent behavioural observation determined that they had been rendered unconscious. In the second experiment, Atlantic salmon parr and smolts were observed for up to 17 min after transiting the commercial stunner to ensure that unconsciousness persisted long enough for death to supervene. Of the 640 fish observed (both in air and water) none showed any signs of recovery. The commercial system and the scaled-down tank used electric fields of 3.1 V/cm and 2.36 V/cm respectively. We conclude that in-water electric stunning can deliver instant and lasting unconsciousness for salmonid juveniles and is well suited for culling operations.

What will happen to my smolt at harvest? Individually tagged Atlantic salmon help to understand possible progression and regression of vertebral deformities

Vertebral deformities can impair health, welfare, and product quality in farmed Atlantic salmon. Deformities detected early in the production cycle raise questions about their further development: which types of deformities will progress and which types of deformities will worsen over time? To study this, Atlantic salmon parr (start experimental feeding weight 13.5 g) were fed diets with low (6.8 g/kg), regular (10.0 g/kg), or high (13.0 g/kg) total dietary P for 11 weeks to provoke deformities. This was followed by long-term monitoring of deformity development up to harvest size (4.5 kg) through repeated radiology of individually tagged animals. Further insights were obtained by histological analyses, mineral analyses, and testing for mechanical properties of vertebral centra. Four categories of deformity development were defined: (1) recovery, (2) containment, (3) progression, and (4) late-onset. Deformities detected early, in freshwater, which affected the vertebral centra but not the intervertebral joints, could fully recover in seawater. These involved low-mineralised vertebrae, single vertically shifted vertebrae, hyper-dense vertebrae (HDV), and two or three adjacent vertebrae with compression-related deformities. HDV were provoked by low dietary P but disappeared in seawater. Fusions were either contained (two to three vertebrae) (stable vertebral fusions) or progressed (more than three vertebrae) (progressive vertebral fusions). Vertical shifts, fusions, and compressions could also have a late-onset in seawater but did not develop into severe deformities in harvest size animals. In conclusion, low-mineralised vertebrae and HDV are abundant in animals with LP diet history but can recover in seawater. The frequency of all other types of deformities was not significantly different among animals of different diet history groups. Under the current experimental conditions, a period of high or low dietary P in freshwater had no significant effect on the prevalence of early- or late-onset deformities at harvest.

Mode of Application of Peracetic Acid-Based Disinfectants has a Minimal Influence on the Antioxidant Defences and Mucosal Structures of Atlantic Salmon (Salmo salar) Parr.

Peracetic acid (PAA) is an oxidative disinfectant with a broad spectrum of antimicrobial activity and low environmental impact. In this study, we investigated the physiological impacts of PAA application in Atlantic salmon (Salmo salar) parr reared in freshwater recirculating aquaculture systems over a 4-week period. PAA at a target concentration of 1 mg/L was administered either in pulse (every 3 days) or continuous. The group that did not receive PAA served as a control. Fish tissue samples were collected for histology, gene expression, and biochemical analyses at day 0 and after 2 and 4 weeks of exposure. The expression of genes encoding for antioxidant defence in the olfactory organs, skin, and gills changed during the trial, but the temporal effects were more pronounced than inter-treatment impacts. The glutathione group of antioxidant genes was more responsive to PAA. In most cases, an upregulation was observed. Significantly lower levels of reactive oxygen species were identified in the plasma and skin mucus of the two PAA-exposed groups at week 4; nonetheless, significantly increased levels of total antioxidant capacity were only observed in the skin mucus of fish from the continuous treatment group. Additional markers of oxidative stress (i.e., 8-oxo-2′-deoxyguanosine and o,o'-dityrosine) were analysed in the skin, gills, liver, and dorsal fins. These markers were unaffected by the two PAA treatments. Sporadic reversible structural alterations were observed in the three mucosal organs; the changes were time-dependent, and the effects of PAA treatment were minimal. The number of mucous cells varied over time but not within treatments except in the skin of the pulse group at week 4 where a reduction was observed. The ratio of acidic and neutral mucous cells in the skin and gills were affected by PAA treatments especially in the pulse group. Overall, this study revealed that Atlantic salmon parr mobilised mucosal and systemic antioxidant defences against the oxidative disinfectant PAA, but it was evident that the mode of application did not impose a strong influence. The minimal effects of PAA application on the indicators of health and welfare underscore the potential use of PAA as a routine disinfectant in recirculating aquaculture systems.

Dietary Inclusion of Hydrolyzed Debaryomyces hansenii Yeasts Modulates Physiological Responses in Plasma and Immune Organs of Atlantic Salmon (Salmo salar) Parr Exposed to Acute Hypoxia Stress.

Stress related to salmon aquaculture practices (handling, sub-optimal nutrition, diseases, and environmental problems) may compromise fish welfare. This study describes the effects of two hydrolyzed Debaryomyces hansenii yeast-based products (LAN4 and LAN6) on physiological and immune responses of Atlantic salmon (Salmo salar) parr exposed to short hypoxia stress. A commercial-like diet (control diet: CD) and two experimental diets (CD supplemented with 0.1% of either component LAN4 or LAN6) were fed to fish for 8 weeks. At the end of the feeding experiment, fish were exposed to 1-min hypoxia and samples were collected at 0, 1, 3, 6, 12, and 24 h post-stress. Results showed that plasma cortisol reached a peak at 1 h post-stress in CD and LAN6 groups, whereas no significant increase in cortisol levels was detected in the LAN4 group. Moreover, the LAN6 group enhanced IL-10 responses to hypoxia, when compared to the control and LAN4 group. This suggests a regulation of immunosuppressive profiles in fish fed LAN4. Hypoxia stress increased TNFα in all groups, which indicates that fish may compensate for the short-term stress response, by modulating innate immune molecules. The apparent suppression of hypoxia responses in the LAN4 group coincided with the detection of differences in goblet cells size and Muc-like proteins production in DI; and upregulation (1 h post-stress) of pathways related to oxygen transport, hemoglobin complex, and glutathione transferase activity and the downregulation of fatty acid metabolism (6 h post-stress) in gills. To conclude, a 1-min hypoxia stress exposure affects the response to stress and immunity; and D. hansenii-based yeast products are promising components in functional aquafeeds for salmon due to their ability to counteract possible consequences of hypoxic stress.

Photoperiod in recirculation aquaculture systems and timing of seawater transfer affect seawater growth performance of Atlantic salmon (Salmo salar)

AbstractProduction of Atlantic salmon smolts in recirculation aquaculture systems (RAS) is growing, and novel production protocols using continuous light in RAS are being implemented in the industry. In the present study, Atlantic Salmon parr were exposed to either a traditional protocol (short‐day winter signal [12:12 L:D] for 6 weeks) or to continuous light. Both photoperiods were applied in freshwater (FW) and brackish water RAS. Salmon from all treatments were transferred to seawater pens at 200 and 600 g and grown until slaughter size. A control group was smoltified with a 6‐week short‐day winter signal and kept in FW until sea transfer at 100 g. Continuous light gave a higher growth rate in RAS but reduced feed intake and growth and increased feed conversion ratio during the first 8 weeks in seawater. However, at slaughter, fish exposed to continuous light was bigger than fish given a winter signal because of the higher growth rate in RAS. Slaughter weight was lowest in fish transferred to sea at 600 g, despite having the highest day‐degree sum during their life span. The best performing group was the control group transferred at 100 g. All treatments handled transfer to seawater and survival and maturation were not affected by the treatments in RAS. The immune status was examined with a multigene expression assay on BioMark HD platform from parr stage to 5–7 months after seawater transfer. Overall, there was no significant effect of photoperiod or salinity on the expression of the selected immune genes. In sum, the results from this study indicate that using continuous light in RAS may have negative effects on performance shortly after transfer in fish transferred to sea at 200 g, whereas at 600 g, all treatments had reduced growth after transfer irrespective of treatment in RAS.

Acute dose-response exposure of a peracetic acid-based disinfectant to Atlantic salmon parr reared in recirculating aquaculture systems

There is a high regard for peracetic acid (PAA)-based disinfectants in recirculating aquaculture systems (RAS) because of the low risk of bioaccumulation, fast degradation with neutral residuals and minimal impact on biofilter performance. However, the no-observed-effect concentration in Atlantic salmon parr is unknown. The present study evaluated the effect of an acute PAA exposure on Atlantic salmon parr health and welfare by evaluating survival, swimming behaviour, appetite and histopathological alterations in the gills and skin. Nine experimental RAS units were employed, where each unit was dedicated for one PAA concentration (0.0, 0.05, 0.1, 0.2, 0.4, 0.8, 1.6, 3.2 and 6.4 mg/L). Fish were exposed to the target PAA concentration in a static system for 1 h and the exposure protocol was repeated after a 52 h recovery. The fish survival was 100%, 80% and 0%, respectively ≤1.6, 3.2 and 6.4 mg/L. Fish swimming behaviour was normal in PAA ≤ 1.6 mg/L, whereas it become erratic with air gasping for PAA ≥ 3.2 mg/L. The fish appetite did not change among the different PAA treatment groups. Skin and gill histopathological alterations were pronounced in PAA ≥ 3.2 mg/L, characterized by a poorer skin condition and necrotic gill lamella. The skin acidic mucous cells density was 55% lower in the 6.4 mg/L group than the 0 mg/L group. The sub-lethal water pH values observed in the 6.4 mg/L group after PAA administration may have played a confounding and compounding factor to the PAA toxicity response in this group. In conclusion, the current study identified the no-observed-effect concentration for PAA to be below 1.6 mg/L for Atlantic salmon parr and provided insights into its use as a water prophylactic strategy in RAS. Toxicity of PAA-based disinfectants is influenced by its acidified nature, which can interfere with the water pH of low alkalinity aquaculture systems. Further studies should evaluate the health and welfare consequences of a long-term PAA exposure in Atlantic salmon parr.

A new look at habitat suitability curves through functional data analysis

Habitat suitability curves (HSC) synthesize the preference of a species for important habitat variables and are, therefore, key components of various fish habitat models. However, HSC are developed at large scales (e.g. river or regional scales) that do not consider the differences that exist in available habitat conditions at smaller scales. To address this problem, a new look at HSC is taken through functional data analysis (FDA). It is an appropriate framework adapted for HSC construction because in FDA, each observation is a curve or a function. To illustrate the potential of FDA for HSC, a dataset of Atlantic salmon (Salmo salar) parr density and habitat variables constructed on two rivers was used. Functional regression models (FRM) were built to predict site-specific HSC based on the available habitat conditions for three salmon parr habitat variables: water depth, mean flow velocity and median substrate size. FRM explained a greater proportion of the variation in site-specific HSC (respectively 38.0%, 53.3% and 45.5% for depth, substrate size and velocity) compared to traditional HSC developed at the scale of each river or regionally that poorly fitted site-specific HSC. When HSC were aggregated into habitat suitability indices (HSI), weak relationships were found between HSI and parr density (R2 < 5%) for all models (traditional HSC and FRM). This study demonstrates that FDA is an innovative framework that can be used to predict more representative site-specific HSC adapted to differences in local available habitat. The results suggested that its potential should be further exploited in habitat modelling.

Impact of dietary zinc and seawater transfer on zinc status, availability, endogenous loss and osmoregulatory responses in Atlantic salmon smolt fed low fish meal feeds

Atlantic salmon fed low fish meal feeds supplemented with zinc (Zn) were studied in two feeding trials. In trial I, Atlantic salmon parr were fed six graded Zn levels (40 to 249 mg kg−1 as ZnSO4) for 8 weeks in freshwater followed by a 4-week seawater phase. In trial II, Atlantic salmon post-smolt were fed for 10 weeks in SW with 10 dietary Zn levels (45 to 280 mg kg−1), either as ZnSO4 or Zn-glycinate. Growth was unaffected by dietary Zn in both trials. Dietary Zn affected concentration of Na + and K+ ions in plasma, branchial and intestinal expression of sodium potassium ATPase, tissue and body Zn status, and cataracts. Seawater transfer significantly reduced apparent availability, body and tissue levels of Zn due to increased endogenous Zn loss. Atlantic salmon post-smolt in seawater improved body and tissue Zn status with increasing dietary Zn levels, irrespective of the Zn source. Body or tissue saturation of Zn occurred at dietary Zn levels between 137 and 156 mg kg−1 with smolts in freshwater and 181 to 218 mg kg−1 in SW post-smolts. Dietary Zn levels below 180 mg kg−1 in low fish meal feeds compromised the Zn status and welfare of Atlantic salmon in seawater.

Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain.

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr.

Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3-V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.

Changes in rearing water microbiomes in RAS induced by membrane filtration alters the hindgut microbiomes of Atlantic salmon (Salmo salar) parr

An important step in water treatment in recirculating aquaculture systems (RAS) is the removal of particulate organic matter. While commonly applied treatment technologies remove most of the particles, fine particulate organic matter typically accumulate in RAS, and serve as substrate for heterotrophic bacteria in the system. Membrane ultrafiltration has been shown to reduce the concentrations of total organic carbon and to counteract blooms of opportunistic bacteria in periods with high organic loading. The potential influence of such opportunistic bacteria on the fish microbiomes and fish welfare is poorly understood. In this study, we investigated the effects of high organic loading on the water and hindgut microbiomes in RAS with Atlantic salmon parr. Two pilot-scale RAS, one with membrane ultrafiltration of a 10–15% side-stream (mRAS), and one without (cRAS), were operated in periods with low and high organic loadings, and the water and hindgut microbiomes were characterized by Illumina sequencing of 16S rDNA amplicons. At the end of the experiment, after a period of high organic loading, two OTUs representing Mycobacterium and Spartobacteria dominated the water microbiomes in cRAS, with relative abundances as high as 24 and 17%, respectively. In the mRAS water they were rare (relative abundances of 1.9 and 0.1%). The membrane ultrafiltration stabilized the water microbiota and efficiently prevented the growth of these bacterial populations in RAS. The parr hindgut microbiomes were generally highly distinct from the RAS water microbiomes and were dominated by the bacterial phyla Bacilli and Firmicutes. Furthermore, an OTU probably representing Carnobacterium inhibens, originally isolated from the gut of adult salmon, was highly abundant in the gut microbiomes, with relative abundances reaching over 30%. However, for the cRAS fish after a period with high organic loading, the relative abundance of this Carnobacterium OTU was reduced, and an increased similarity between the gut and the water microbiomes was observed. The Mycobacterium and Spartobacteria OTUs that were abundant in the cRAS water were also abundant in the cRAS hindgut samples. This indicates a direct influence of the water microbiomes on the gut microbiomes, and that high organic loading in the cRAS resulted in growth of opportunistic bacteria that were able to colonize the fish gut. The present study shows that membrane filtration is an applicable strategy to counteract growth of opportunistic bacteria in RAS and to promote positive fish – microbe interactions.

Microbial community dynamics in a commercial RAS for production of Atlantic salmon fry (Salmo salar)

Recirculating aquaculture systems (RAS) harbour complex microbial communities which can have an impact on the growth and development of the reared fish. This study aimed to improve our understanding of microbial community dynamics in a RAS involving three production batches of Atlantic salmon fry and parr during a period of 20 months. Water for analysis of microbiota was sampled at different positions in the RAS, and we also examined the effect of UV treatment on the water microbiota. Microbial communities were characterized by 16S rDNA amplicon sequencing of water samples taken directly upstream and downstream of the UV treatment unit and from three of the rearing tanks. In total 6 sampling events were made during a 20-month period. The study showed that: 1) Two of the production batches had a highly similar water microbiota despite disinfection of the system between the batches and rearing fish of different stages. In contrast, the first production batch showed a different water microbiota with variable composition through the system and over time. A more immature biofilter in the first batch may explain these differences. 2) The full-flow UV treatment directly upstream the rearing tanks had no observable effect on the community composition of the water microbiota in the different sampling positions in the RAS. This was likely a consequence of the low hydraulic retention time (HRT) (23 min) in rearing tanks, low bacterial regrowth in the fish tanks and community changes throughout the RAS loop. 3) The disinfection effect on viable bacterial densities in the water directly downstream of the UV treatment was around 89%, when the water was clear. Regrowth of bacteria following disinfection was low compared to those reported for marine RAS with UV disinfection and long HRT in fish tanks. The study shows that UV disinfection can be used to efficiently reduce bacterial density without compromising the microbial water quality in the fish tanks in RAS with low HRT.

Dietary electrolyte balance of Atlantic salmon (Salmo salar) freshwater feeds: Impact on osmoregulation, mineral metabolism and performance in seawater

Dietary electrolyte balance is the equilibrium of monovalent cations and anions that influence the acid-base balance of the feed (dEB = Na + K − Cl, mEq kg−1). Dietary electrolytes/minerals can influence the physiological changes during smoltification in Atlantic salmon. In this context, we aimed to study if the dEB of the freshwater feeds can be used to pre-adapt the hypoosmotic functionality and the associated effects on mineral metabolism. The dEB of commercial freshwater Atlantic salmon feeds in Norway varied from −9 to 400 mEq kg−1 feed. Three experimental feeds were formulated to study incremental levels of dEB reflecting the low (L-dEB, −50 to 0), median (M-dEB, 200–250) and high (H-dEB, 350–400). Triplicate groups of Atlantic salmon parr (36 g) were fed one of the three feeds for 8 weeks in freshwater at 12 °C. The fish were transferred to full strength seawater in indoor tanks and fed a commercial diet for 6 weeks. Growth was not differentially affected by dEB levels, neither in the freshwater phase nor in the seawater. Plasma electrolytes (Na+ and Cl−) and gill mRNA expression of sodium potassium ATPase (NKA a1b, seawater isoform) were significantly lower in L-dEB fed fish. In the intestine, carbonate precipitates 24 h after seawater transfer was higher in fish fed both L-dEB and H-dEB feeds compared to the M-dEB fed fish. Whole body and plasma mineral levels were significantly affected by dEB levels in freshwater feeds. Interestingly, the carryover effect of dEB in freshwater feeds was significant after 6 weeks in seawater for plasma and whole-body Zn status, with the H-dEB fed fish showing significantly increased body Zn status compared to L-dEB and M-dEB fed fish. The study revealed that mineral metabolism and intestinal response to seawater transfer can be pre-adapted by modulating the electrolyte and/or mineral balance in freshwater feeds in Atlantic salmon. Further, dEB did not affect long term development of cataract or vertebral deformities.

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

BackgroundInfectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing.ResultsA total of 2833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1353 animals were genotyped using a 55 K SNP array, and the estimate of heritability for the trait of binary survival was 0.13–0.33 (pedigree-genomic). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome Ssa13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated in infected fish, while several metabolic pathways were up-regulated. The interferon pathway showed little evidence of up-regulation at 7 days post infection but was mildly activated at 14 days, suggesting a potential crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish.ConclusionsISAV resistance shows moderate heritability with a polygenic architecture, but a significant QTL was detected on chromosome 13. A mild up-regulation of the interferon pathway characterises the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.

Vertebral column adaptations in juvenile Atlantic salmon Salmo salar, L. as a response to dietary phosphorus

Deficiency in dietary phosphorus (P) is considered as a nutritional risk factor for the development of vertebral column deformities in farmed Atlantic salmon Salmo salar, L. This mono-factorial study examines how 11-week deficiency and excess of dietary P influence the structure and microstructure of the vertebral bodies in juvenile, freshwater stages of Atlantic salmon. Animals were fed continuously with three diets containing different levels of total P (tP) and soluble P (sP), respectively: low P (LP) = 6.8 g/kg tP, 3.5 g/kg sP, regular P (RP) = 10.0 g/kg tP, 5.6 g/kg sP, and high P (HP) = 13.0 g/kg tP, 9.3 g/kg sP. Animals were analysed for plasma and bone mineral content, vertebral column deformities (x-ray), vertebral centra stiffness, bone mineralisation pattern and vertebral body microanatomy (cells and connective tissue structures). A low (background) level of deformities was observed on a gross morphological level but no increase and no specific type of vertebral column deformity was associated with either of the three groups. While feed intake was comparable among all diet groups animals fed LP showed a 50% reduction in total calcium (Ca) and P content in abdominal vertebrae and opercula. Regular P and HP animals showed similar levels of total Ca and P in abdominal vertebrae and opercula. Animals in all diet groups showed well-developed vertebral bodies. Low P animals had vertebral centra, neural and haemal arches with large areas of non-mineralised bone. Vertebral centra stiffness in LP animals was reduced accordingly. Regular P and HP animals showed comparable values for vertebral centra stiffness. Non-mineralised vertebral body end plates of LP animals developed a slight inward bending and intervertebral ligaments increased in length and thickness. The cellular and extracellular components of the intervertebral joints remained intact without structural alterations that would indicate the development of vertebral centra compression or fusion. Animals from all three diet groups showed active osteoblasts at the vertebral body growth zone. Despite the three-fold decline in plasma inorganic P in LP animals growth continued at the same rate as in RP and HP animals. It is discussed whether the use of a P-reduced diet under a continuous feeding regime can maintain growth without adverse effects for animal health and welfare. This study further discusses that a HP diet relative to an RP diet has no beneficial effect concerning bone formation, bone mineralisation, growth and prevention of vertebral centra deformities in Atlantic salmon parr.

Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon.

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population‐level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.