Characterising the Physiological Responses of Chinook Salmon (Oncorhynchus tshawytscha) Subjected to Heat and Oxygen Stress.

In New Zealand, during the hottest periods of the year, some salmon farms in the Marlborough Sounds reach water temperatures above the optimal range for Chinook salmon. High levels of mortality are recorded during these periods, emphasising the importance of understanding thermal stress in this species. In this study, the responses of Chinook salmon (Oncorhynchus tshawytscha) to chronic, long-term changes in temperature and dissolved oxygen were investigated. This is a unique investigation due to the duration of the stress events the fish were exposed to. Health and haematological parameters were analysed alongside gene expression results to determine the effects of thermal stress on Chinook salmon. Six copies of heat shock protein 90 (HSP90) were discovered and characterised: HSP90AA1.1a, HSP90AA1.2a, HSP90AA1.1b, HSP90AA1.2b, HSP90AB1a and HSP90AB1b, as well as two copies of SOD1, named SOD1a and SOD1b. The amino acid sequences contained features similar to those found in other vertebrate HSP90 and SOD1 sequences, and the phylogenetic tree and synteny analysis provided conclusive evidence of their relationship to other vertebrate HSP90 and SOD1 genes. Primers were designed for qPCR to enable the expression of all copies of HSP90 and SOD1 to be analysed. The expression studies showed that HSP90 and SOD1 were downregulated in the liver and spleen in response to longer term exposure to high temperatures and lower dissolved oxygen. HSP90 was also downregulated in the gill; however, the results for SOD1 expression in the gill were not conclusive. This study provides important insights into the physiological and genetic responses of Chinook salmon to temperature and oxygen stress, which are critical for developing sustainable fish aquaculture in an era of changing global climates.

Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates.

Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.

Modeling the effects of ration on individual growth of Oncorhynchus tshawytscha under controlled conditions.

Fed aquaculture is one of the fastest-growing and most valuable food production industries in the world. The efficiency with which farmed fish convert feed into biomass influences both environmental impact and economic revenue. Salmonid species, such as king salmon (Oncorhynchus tshawytscha), exhibit high levels of plasticity in vital rates such as feed intake and growth rates. Accurate estimations of individual variability in vital rates are important for production management. The use of mean trait values to evaluate feeding and growth performance can mask individual-level differences that potentially contribute to inefficiencies. Here, the authors apply a cohort integral projection model (IPM) framework to investigate individual variation in growth performance of 1625 individually tagged king salmon fed one of three distinct rations of 60%, 80%, and 100% satiation and tracked over a duration of 276 days. To capture the observed sigmoidal growth of individuals, they compared a nonlinear mixed-effects (logistic) model to a linear model used within the IPM framework. Ration significantly influenced several aspects of growth, both at the individual and at the cohort level. Mean final body mass and mean growth rate increased with ration; however, variance in body mass and feed intake also increased significantly over time. Trends in mean body mass and individual body mass variation were captured by both logistic and linear models, suggesting the linear model to be suitable for use in the IPM. The authors also observed that higher rations resulted in a decreasing proportion of individuals reaching the cohort's mean body mass or larger by the end of the experiment. This suggests that, in the present experiment, feeding to satiation did not produce the desired effects of efficient, fast, and uniform growth in juvenile king salmon. Although monitoring individuals through time is challenging in commercial aquaculture settings, recent technological advances combined with an IPM approach could provide new scope for tracking growth performance in experimental and farmed populations. Using the IPM framework might allow the exploration of other size-dependent processes affecting vital rate functions, such as competition and mortality.

Molecular evidence for stress, inflammation and structural changes in non-specific ulcers in skin of farmed Chinook salmon (Oncorhynchus tshawytscha).

Fish skin is critical to physical defence against pathogens and there is a need to understand the physiological processes impacting ulcers and their healing. Ulcers have been reported in farmed Chinook salmon in New Zealand. This study investigated stress, immune and structural gene expression in farmed Chinook salmon skin with and without ulcers from two sites in New Zealand sampled from February (higher temperature, late summer) to May (lower temperature, late autumn). Skin samples taken adjacent to non-specific ulcers in May and control fish in February demonstrated upregulation of heat shock protein 70 relative to control fish in May. Anterior gradient 2 expression was upregulated in fish with ulcers relative to control fish (both February and May), suggesting increased mucous cell activity. Based on the results of this study, fish with non-specific ulcers showed evidence of stress, inflammation, re-epithelisation, and delayed healing near the ulcer site, elucidating the importance of these processes in the pathogenesis of non-specific ulcers in farmed chinook salmon.

The influence of temperature on performance, biological indices, composition, and nutrient retention of juvenile Chinook salmon (Oncorhynchus tshawytscha) reared in freshwater.

This study investigated the effects of different temperatures on the performance, composition, and nutrient retention of Chinook salmon reared in freshwater. Individuals (187.6 ± 27.1 g) were distributed into twelve tanks of 8000 L each (155 to 157 fish per tank) at a temperature of 14 °C. The tanks were transitioned from 14 °C (hatchery temperature) to 8, 12, 16, and 20 °C over seven days. Three fish assessments were performed, the first (initial) when the fish were distributed in the tanks, a second (interim) between days 9 and 16 at the start of the experiment, and a third (final) after 41 to 49 days at the target temperature. At the end of the trial, performance parameters, proximate composition, amino acid, and fatty acid composition, and nutrient retention were evaluated. Better growth performance was observed in fish at 16 °C and 20 °C compared to the lower temperatures. Fish at higher temperatures had higher levels of saturated fatty acids (SFA), while at lower temperatures fish had higher levels of n-3 and n-6 polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). A polynomial relationship between nutrient retention and temperature showed that fish from all treatments retained more lipids than proteins, with higher retention of MUFA compared to the other fatty acid classes. Additionally, DHA retention was approximately three times higher than EPA retention. The results showed that 16 to 20 °C was the optimum temperature range for Chinook salmon, and the performance differences were mainly modulated by lipid retention/catabolism.

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems.

Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.

The relationships between specific dynamic action, nutrient retention and feed conversion ratio in farmed freshwater Chinook salmon (Oncorhynchus tshawytscha).

Improving the feed conversion ratio (FCR; the amount of feed consumed relative to the amount of weight gain) can reduce both production costs and environmental impacts of farmed fish. The aim of this study was to investigate what drives FCR to understand how nutrients are retained, as well as the amount of oxygen consumed for digestion, absorption and assimilation (a metabolic process known as specific dynamic action, SDA). Feed-efficient and inefficient Chinook salmon (Oncorhynchus tshawytscha) in fresh water were identified using ballotini beads and X-radiography that tracked individual feed intake across three assessment periods under satiated feeding. This allowed a comparison of physiological traits and body composition between the two FCR phenotypes over two time points as Chinook salmon grew from 305 to 620 g. Fish with higher daily feed intake (DFI) had higher daily weight gain (DWG) as expected. Nonetheless, the relationship between FCR and DFI as well as FCR and DWG was variable between time points. FCR and DWG were not correlated at the first time point and were negatively correlated at the second time point. In contrast, FCR and DFI were positively correlated at the first time point but not the second. Despite this, efficient fish ate smaller meals and retained more protein, lipid and energy in their body tissues. There was no detectable difference in metabolism between the two FCR phenotypes with respect to minimal resting metabolic rate, maximum metabolic rate, aerobic scope, or SDA parameters. In conclusion, FCR is not consistently associated with growth and metabolic differences in freshwater Chinook salmon, but FCR-efficient fish retain more nutrients and consume smaller meals.

Protein metabolism in the liver and white muscle is associated with feed efficiency in Chinook salmon (Oncorhynchus tshawytscha) reared in seawater: Evidence from proteomic analysis.

Understanding the molecular mechanisms that underlie differences in feed efficiency (FE) is an important step toward optimising growth and achieving sustainable salmonid aquaculture. In this study, the liver and white muscle proteomes of feed efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) reared in seawater were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 2746 liver and 702 white muscle proteins were quantified and compared between 21 EFF and 22 INEFF fish. GSEA showed that gene sets related to protein synthesis were enriched in the liver and white muscle of the EFF group, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. Estimates of individual daily feed intake and share of the meal within tank were significantly higher in the INEFF than the EFF fish showing INEFF fish were likely more dominant during feeding and overfed. Overeating by the INEFF fish was associated with an increase in protein catabolism. This study found that fish with different FE values had expression differences in the gene sets related to protein turnover, and this result supports the hypothesis that protein metabolism plays a role in FE.

Transcriptomic characterisation of a common skin lesion in farmed chinook salmon.

Little is known about host responses of farmed Chinook salmon with skin lesions, despite the lesions being associated with increased water temperatures and elevated mortality rates. To address this shortfall, a transcriptomic approach was used to characterise the molecular landscape of spot lesions, the most commonly reported lesion type in New Zealand Chinook salmon, versus healthy appearing skin in fish with and without spot lesions. Many biological (gene ontology) pathways were enriched in lesion adjacent tissue, relative to control skin tissue, including proteolysis, fin regeneration, calcium ion binding, mitochondrial transport, actin cytoskeleton organisation, epithelium development, and tissue development. In terms of specific transcripts of interest, pro-inflammatory cytokines (interleukin 1ß and tumour necrosis factor), annexin A1, mucin 2, and calreticulin were upregulated, while cathepsin H, mucin 5AC, and perforin 1 were downregulated in lesion tissue. In some instances, changes in gene expression were consistent between lesion and healthy appearing skin from the same fish relative to lesion free fish, suggesting that host responses weren't limited to the site of the lesion. Goblet cell density in skin histological sections was not different between skin sample types. Collectively, these results provide insights into the physiological changes associated with common spot lesions in farmed Chinook salmon.

Effects of fasting and temperature on the biological parameters, proximal composition, and fatty acid profile of Chinook salmon (Oncorhynchus tshawytscha) at different life stages.

We investigated the effects of temperature and fasting on chinook salmon (Oncorhynchus tshawytscha) at different life stages. In the first stage, fish were reared at 13 °C (198.5 ± 34.6 g) or 17 °C (218.3 ± 47.6 g) and fasted for 27 and 26 days, respectively. In the second stage, fish reared at 13 °C (481.8 ± 54.3 g) and 17 °C (597.3 ± 64.3 g) were fasted for 42 and 41 days respectively. At the third stage, fish were reared only at 17 °C (1065.7 ± 190.9 g) and fasted for 42 days. At the end of each fasting period performance, fillet and whole-body proximal composition, and whole-body fatty acid profile were compared among fish before and after fasting. Additionally, fillet fatty acid daily loss was compared in fasted fish from different treatments. The results showed that body weight was not significantly impacted by fasting. However, at 17 °C fasting at all three stages had a negative impact on fillet weight and total fatty acid daily loss. With few exceptions, saturated (SFA), monounsaturated (MUFA) and polyunsaturated fatty acids from n-6 series (n-6 PUFA) were preserved in fillet of fish at 17 °C, while higher daily losses of docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and consequently polyunsaturated from n-3 series (n-3 PUFA) were observed in these same fish and in smaller fish at 13 °C. The results presented in this study provide important information regarding the influence of fasting and temperature on chinook salmon performance and metabolism, providing basis for future nutritional and compositional studies for this important commercial species.

Uncoupling Thermotolerance and Growth Performance in Chinook Salmon: Blood Biochemistry and Immune Capacity.

Ocean warming and extreme sea surface temperature anomalies are threatening wild and domesticated fish stocks in various regions. Understanding mechanisms for thermotolerance and processes associated with divergent growth performance is key to the future success of aquaculture and fisheries management. Herein, we exposed Chinook salmon (Oncorhynchus tshawytscha) to environmentally relevant water temperatures (19-20 °C) approaching their upper physiological limit for three months and sought to identify blood biomarkers associated with thermal stress and resilience. In parallel, blood biochemical associations with growth performance were also investigated. Temperature stress-activated leukocyte apoptosis induced a minor immune response, and influenced blood ion profiles indicative of osmoregulatory perturbation, regardless of how well fish grew. Conversely, fish displaying poor growth performance irrespective of temperature exhibited numerous biomarker shifts including haematology indices, cellular-based enzyme activities, and blood clinical chemistries associated with malnutrition and disturbances in energy metabolism, endocrine functioning, immunocompetence, redox status, and osmoregulation. Findings provide insight into mechanisms of stress tolerance and compromised growth potential. Biochemical phenotypes associated with growth performance and health can potentially be used to improve selective breeding strategies.

Case definitions for skin lesion syndromes in chinook salmon farmed in Marlborough Sounds, New Zealand.

Skin lesions are commonly reported in farmed salmonids. Chinook salmon (Oncorhynchus tshawytscha), introduced from California USA, is the only salmonid species commercially farmed in New Zealand, although trout are cultured for release by Fish and Game New Zealand. There are several farming areas in New Zealand, including Marlborough Sounds, Canterbury and Stewart Island. While the industry has not been affected by any of the major production diseases seen internationally, skin lesions have been recorded with an increase in prevalence from 2012 onwards in the Marlborough Sounds and were associated with elevated summer mortalities on farms in 2015. Here we are proposing case definitions for different types of skin lesions for future monitoring and research. Based on our current understanding of the above skin conditions, we developed case definitions for spots, spreading spots, ulcerated spreading spots and Regular Outline Flank Ulcers defining a positive case for three study units, including individual fish, pen/unit and farm.

Impact of acute handling stress, anaesthesia, and euthanasia on fish plasma biochemistry: implications for veterinary screening and metabolomic sampling.

Impacts of pre-sampling practices on fish plasma biochemistry may bias the outcome of a study if not considered within the general sampling strategy. Acute handling stresses can be imposed on fish during capture, and it is common practice to immobilise fish via sedation prior to obtaining blood samples for non-lethal extraction purposes, and/or to reduce stress, pain, or suffering before being euthanised. We investigated these potential influences using a Chinook salmon model (Oncorhynchus tshawytscha) by measuring levels of 119 biochemical targets comprising ions, metabolites, and enzymes in plasma. Multivariate analyses showed that 2 min of confinement with mild handling manipulation led to a significant departure from baseline metabolism, which was further exasperated during a prolonged 5-min challenge. These changes were characterised by a disruption in osmoregulation, a switch towards anaerobic metabolism, and shifts in ammonia recycling, among others. Sedation of fish with clove oil and AQUI-S® had major impacts on plasma biochemical profiles, with alterations signalling changes in glycolytic metabolism, respiratory modes, carbon flux through the TCA cycle, and lipid compartmentalisation. Sedation also enhanced levels of plasma amino acids, revealing a key difference between responses to handling stress and sedation. These results demonstrate that pre-harvest practices should be carefully managed during fish sampling for biochemical/metabolomic-based analyses, and if manipulations are essential, they should be standardised.

Developing Successful Breeding Programs for New Zealand Aquaculture: A Perspective on Progress and Future Genomic Opportunities.

Over the past 40 years New Zealand (NZ) aquaculture has grown into a significant primary industry. Tonnage is small on a global scale, but the industry has built an international reputation for the supply of high quality seafood to many overseas markets. Since the early 1990s the industry has recognized the potential gains from selective breeding and the challenge has been to develop programs that can overcome biological obstacles (such as larval rearing and mortality) and operate cost-effectively on a relatively small scale while still providing significant gains in multiple traits of economic value. This paper provides an overview of the current status, and a perspective on genomic technology implementation, for the family based genetic improvement programs established for the two main species farmed in NZ: Chinook (king) salmon (Oncorhynchus tshawytscha) and GreenshellTM mussel (Perna canaliculus). These programs have provided significant benefit to the industry in which we are now developing genomic resources based on genotyping-by-sequencing to complement the breeding programs, enable evaluation of the genetic diversity and identify the potential benefits of genomic selection. This represents an opportunity to increase genetic gain and more effectively utilize the potential for within family selection.

Unilateral perivertebral fibrosis associated with lordosis, kyphosis and scoliosis (LKS) in farmed Chinook salmon in New Zealand.

Vertebral column lordosis, kyphosis and scoliosis (LKS) can result in downgrading of farmed Chinook salmon Oncorhynchus tshawytscha in New Zealand. No cause of LKS has been identified. Radiography and histology were used to quantify LKS and perivertebral fibrosis in 27 fish with LKS visible at harvest and 30 visually normal fish from 3 New Zealand farms. Radiographic LKS was present in all 27 fish with LKS and in 18 of 30 fish without visible LKS. Quantification of the radiographic severity revealed significantly higher radiographic severity scores in fish with visible LKS (mean ± SD = 5.89 ± 2.41) than in fish with no visible, but radiographic LKS (1.44 ± 0.86, p < 0.001). The most frequent histological finding was unilateral perivertebral fibrosis that often extended into the horizontal septum and adjacent myomeres resulting in separation or loss of myocytes. Fibrosis was visible in all fish with LKS and in 12 of 30 fish without visible LKS. Fibrosis scores were higher in fish with visible LKS (3.32 ± 1.71) than in fish without visible LKS (0.35 ± 0.57, p < 0.001). The radiographic LKS severity scores were significantly correlated to the fibrosis scores (R2 = 0.59 p < 0.001) in the fish. Histology of other tissues revealed multifocal inflammation within muscle, peripheral connective tissues and myocardium which were considered most likely incidental in these fish. In this study, LKS was consistently and significantly associated with perivertebral fibrosis, suggesting that perivertebral fibrosis is an important process in the development of LKS. Further research to determine the cause of the fibrosis is required.

Accommodating the cost of growth and swimming in fish-the applicability of exercise-induced growth to juvenile hapuku (Polyprion oxygeneios).

Induced-swimming can improve the growth and feed conversion efficiency of finfish aquaculture species, such as salmonids and Seriola sp., but some species, such as Atlantic cod, show no or a negative productivity response to exercise. As a possible explanation for these species-specific differences, a recent hypothesis proposed that the applicability of exercise training, as well as the exercise regime for optimal growth gain (ERopt growth), was dependent upon the size of available aerobic metabolic scope (AMS). This study aimed to test this hypothesis by measuring the growth and swimming metabolism of hapuku, Polyprion oxygeneios, to different exercise regimes and then reconciling the metabolic costs of swimming and specific dynamic action (SDA) against AMS. Two 8-week growth trials were conducted with ERs of 0.0, 0.25, 0.5, 0.75, 1, and 1.5 body lengths per second (BL s(-1)). Fish in the first trial showed a modest 4.8% increase in SGR over static controls in the region 0.5-0.75 BL s(-1) whereas the fish in trial 2 showed no significant effect of ER on growth performance. Reconciling the SDA of hapuku with the metabolic costs of swimming showed that hapuku AMS is sufficient to support growth and swimming at all ERs. The current study therefore suggests that exercise-induced growth is independent of AMS and is driven by other factors.

Comparative genomic analysis of Atlantic salmon, Salmo salar, from Europe and North America.

BACKGROUND: Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing of mtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from North America and Europe are genetically distinct. These observations are supported by karyotype analysis, which revealed that North American Atlantic salmon have 27 pairs of chromosomes whereas European salmon have 29 pairs. We set out to construct a linkage map for a North American Atlantic salmon family and to compare this map with the well developed map for European Atlantic salmon. RESULTS: We used microsatellite markers, which had previously been mapped in the two Atlantic salmon SALMAP mapping families from the River Tay, Scotland, to carry out linkage analysis in an Atlantic salmon family (NB1) whose parents were derived from the Saint John River stock in New Brunswick, Canada. As large differences in recombination rates between female and male Atlantic salmon have been noted, separate genetic maps were constructed for each sex. The female linkage map comprises 218 markers in 37 linkage groups while the male map has 226 markers in 28 linkage groups. We combined 280 markers from the female and male maps into 27 composite linkage groups, which correspond to the haploid number of chromosomes in Atlantic salmon from the Western Atlantic. CONCLUSIONS: A comparison of the composite NB1 and SALMAP linkage maps revealed the reason for the difference in the chromosome numbers between European and North American Atlantic salmon: Linkage groups AS-4 and AS-32 in the Scottish salmon, which correspond to chromosomes Ssa-6 and Ssa-22, are combined into a single NB1 linkage group as are linkage groups AS-21 and AS-33 (corresponding to chromosomes Ssa-26 and Ssa-28). The comparison of the linkage maps also suggested some additional chromosomal rearrangements, but it will require finer mapping, potentially using SNPs, to test these predictions. Our results provide the first comparison of the genomic architecture of Atlantic salmon from North America and Europe with respect to chromosome organization.