Atlantic Salmon In Scotland Research Articles

Monitoring monthly mortality of maricultured Atlantic salmon (Salmo salar L.) in Scotland II. A hierarchical dynamic linear model

The sustainability of the salmon farming industry is being challenged by increased mortality rates. Scotland’s open-source salmon production data provides the possibility of developing an industry-wide mortality monitoring model, valuable for identifying and addressing unexpected increases in mortality without needing data sharing agreements across different companies. This study aimed to utilize these data to develop a hierarchical dynamic linear model (DLM) for monitoring monthly mortality of maricultured Atlantic salmon in Scotland. We evaluated whether considering the hierarchical structure present in the data (country, region, and site) would improve mortality predictions when compared to the production cycle level DLMs developed in a previous study. Our findings demonstrated that the hierarchical DLM outperformed the production cycle level DLMs, confirming the value of this more complex modelling approach. Nevertheless, the hierarchical model, like the production cycle level DLMs, exhibited some uncertainty in the mortality predictions. When mortality is higher than expected, site level warnings are generated, which can encourage producers and inspectors to further investigate the cause. Between 2015 and 2020, approximately 25% of the production cycles and 50% of the sites encountered at least one warning, with most warnings happening in the summer and autumn months. Additionally, the hierarchical model enabled monitoring mortality at multiple levels. This information is useful for various stakeholders as part of a monitoring system, offering insights into mortality trends at national, regional, and sites levels that may benefit from strategic resource management. Recommendations for model improvements include utilizing shorter data aggregation periods, such as weekly, which are not currently available as open-source data.

Monitoring monthly mortality of maricultured Atlantic salmon (Salmo salar L.) in Scotland I. Dynamic linear models at production cycle level

The mortality of Atlantic salmon is one of the main challenges to achieving its sustainable production. This sector benefits from generating many data, some of which are collated in a standardized way, on a monthly basis at site level, and are accessible to the public. This continuously updated resource might provide opportunities to monitor mortality and prompt producers and inspectors to further investigate when mortality is higher than expected. This study aimed to use the available open-source data to develop production cycle level dynamic linear models (DLMs) for monitoring monthly mortality of maricultured Atlantic salmon in Scotland. To achieve this, several production cycle level DLMs were created: one univariate DLM that includes just mortality; and various multivariate DLMs that include mortality and different combinations of environmental variables. While environmental information is not collated in a standardized way across all sites, open-source remote-sensed satellite resources provide continuous, standardized estimates. By combining environmental and mortality data, we seek to investigate whether adding environmental variables enhanced the estimates of mortality, and if so, which variables were most informative in this respect. The multivariate model performed better than the univariate DLM (P = .004), with salinity as the only significant contributor out of 12 environmental variables. Both models exhibited uncertainty related to the mortality estimates. Warnings were generated when any observation fell above the 95% credible interval. Approximately 30% of production cycles and more than 50% of sites experienced at least one warning between 2015 and 2020. Occurrences of these warnings were non-uniformly distributed across space and time, with the majority happening in the summer and autumn months. Recommendations for model improvement include employing shorter time periods for data aggregation, such as weekly instead of on a monthly basis. Furthermore, developing a model that takes hierarchical relationships into account could offer a promising approach.

Salmonid Alphavirus (SAV).

Salmonid alphavirus (SAV), genus Alphavirus, family Togaviridae, is a single-stranded RNA virus affecting Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). It is known to be responsible for pancreas disease (PD) and sleeping disease (SD) which are increasing problems, causing high fish mortality and economic losses in the European aquaculture industry. Pancreas disease was first described in Atlantic salmon in Scotland in 1976 and a similar disease caused by the closely related sleeping disease virus was first described in rainbow trout in France. There have also been reports of salmonid alphavirus infections from other European countries, including Ireland, England, Norway, Germany, Italy, and Spain. Salmonid alphaviruses have been classified into six subtypes (SAV1–6). SAV1 and SAV4–6 cause pancreas disease in Atlantic salmon in Ireland or Scotland, SAV2 is the causative agent of sleeping disease in rainbow trout, and SAV3 has been detected in Atlantic salmon in Norway. The aim of this paper was to summarise current knowledge of infections caused by salmonid alphavirus and diagnostic methods including the newest techniques, and to briefly describe prevention from SAV infections by vaccination.

Efficacy and safety of a non-mineral oil adjuvanted injectable vaccine for the protection of Atlantic salmon (Salmo salar L.) against Flavobacterium psychrophilum

Flavobacterium psychrophilum is the causative agent of Rainbow Trout Fry Syndrome which has had a major impact on global salmonid aquaculture. Recent outbreaks in Atlantic salmon in Scotland and Chile have added to the need for a vaccine to protect both salmon and trout. At present no licensed vaccines are available in Europe, leaving antibiotics as the only course of action to contain disease outbreaks. Outbreaks generally occur in fry at temperatures between 10 and 15 °C. Recently outbreaks in larger fish have given added impetus to the development of a vaccine which can provide long term protection from this highly heterogeneous pathogen. Most fish injectable vaccines are formulated with oil emulsion adjuvants to induce strong and long lasting immunity, but which are known to cause side effects. Alternative adjuvants are currently sought to minimise these adverse effects.The current study was performed to assess the efficacy of a polyvalent, whole cell vaccine containing formalin-inactivated F. psychrophilum to induce protective immunity in Atlantic salmon. The vaccine was formulated with an adjuvant containing squalene and aluminium hydroxide, and was compared to a vaccine formulated with a traditional oil adjuvant, Montanide ISA 760VG, and a non-adjuvanted vaccine. Duplicate groups of salmon (23.5 ± 6.8 g) were vaccinated with each of the vaccine formulations or phosphate buffered saline by intraperitoneal injection. Fish were challenged by intramuscular injection with F. psychrophilum six weeks post-vaccination to test the efficacy of the vaccines. Cumulative mortality reached 70% in the control salmon, while the groups of salmon that received vaccine had significantly lower mortality than the controls (p = 0.0001), with no significant difference in survival between vaccinated groups. The squalene/alum adjuvant was safe, more readily metabolised by the fish and induced less histopathological changes than the traditional oil adjuvant.

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers.

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.

Yersinia ruckeri Isolates Recovered from Diseased Atlantic Salmon (Salmo salar) in Scotland Are More Diverse than Those from Rainbow Trout (Oncorhynchus mykiss) and Represent Distinct Subpopulations.

Yersinia ruckeri is the etiological agent of enteric redmouth (ERM) disease of farmed salmonids. Enteric redmouth disease is traditionally associated with rainbow trout (Oncorhynchus mykiss, Walbaum), but its incidence in Atlantic salmon (Salmo salar) is increasing. Yersinia ruckeri isolates recovered from diseased Atlantic salmon have been poorly characterized, and very little is known about the relationship of the isolates associated with these two species. Phenotypic approaches were used to characterize 109 Y. ruckeri isolates recovered over a 14-year period from infected Atlantic salmon in Scotland; 26 isolates from infected rainbow trout were also characterized. Biotyping, serotyping, and comparison of outer membrane protein profiles identified 19 Y. ruckeri clones associated with Atlantic salmon but only five associated with rainbow trout; none of the Atlantic salmon clones occurred in rainbow trout and vice versa These findings suggest that distinct subpopulations of Y. ruckeri are associated with each species. A new O serotype (designated O8) was identified in 56 biotype 1 Atlantic salmon isolates and was the most common serotype identified from 2006 to 2011 and in 2014, suggesting an increased prevalence during the time period sampled. Rainbow trout isolates were represented almost exclusively by the same biotype 2, serotype O1 clone that has been responsible for the majority of ERM outbreaks in this species within the United Kingdom since the 1980s. However, the identification of two biotype 2, serotype O8 isolates in rainbow trout suggests that vaccines containing serotypes O1 and O8 should be evaluated in both rainbow trout and Atlantic salmon for application in Scotland. Vaccination plays an important role in protecting Atlantic salmon against the bacterial pathogen Yersinia ruckeri, but, in recent years, there has been an increasing incidence of vaccine breakdown in salmon. This is largely because current vaccines are aimed at rainbow trout and are based on serotypes specific for this species. A wider range of serotypes is responsible for infection in Atlantic salmon, but very little is known about the diversity of these strains and their relationships to those recovered from rainbow trout. In the present study, we demonstrate that Y. ruckeri isolates recovered from diseased Atlantic salmon in Scotland are more diverse than those from rainbow trout; furthermore, isolates from the two species represent distinct subpopulations. In addition, a new O serotype was identified that is responsible for a significant proportion of the disease in Atlantic salmon. Our findings are likely to have important implications for the development of improved vaccines against Y. ruckeri.

A note on sea lice abundance on farmed Atlantic salmon in Scotland 2011-2013: significant regional and seasonal variation

Sea lice are the most economically damaging parasite affecting marine Atlantic salmon production the dominant sector of UK aquaculture. The Scottish Salmon Producers' Organisation has published mean adult female lice abundance for four regions for 2011–2013 and for 30 areas in 2013. An analysis of these data shows that sea lice abundance is highly seasonal with values lowest in the first half of the year. Abundance also varies by region, the regional patterns vary from year-to-year but overall the highest abundance was found in the northern part of mainland Scotland. While most areas had low lice abundance, in a few areas the abundance was persistently above average; these areas were clustered together. There was no significant year-on-year trend in lice abundance, and trends appear to vary between regions. Although previous Scottish analyses have been carried out using data from a large company, this analysis cover 95% of production in all salmon farming regions of Scotland and it can be extended as more data become available.

Form and uncertainty in stock–recruitment relations: observations and implications for Atlantic salmon (Salmo salar) management

This paper reports an investigation of stock–recruitment relations for Atlantic salmon ( Salmo salar ). We regard these relations as stochastic functions characterized by an expected stock–recruitment relation and deviations from this expectation driven by observational error and uncharacterised environmental variability. We estimate model parameters by standard Bayesian methods. Analysis of the input–output characteristics of segments of the salmon life cycle in the Girnock Burn (Northeast Scotland) reveals two independent regulatory processes, one between ova and fry and the other between fry and smolts. Comparison of stock–recruitment relations for Atlantic salmon in Scotland, Ireland, and Canada, reinforced by an extended series of simulation studies, shows that even when comparatively long time series of high quality data are available, it is frequently difficult to exclude the possibility of low stock depensation — an effect whose implication of enhanced extinction risk implies that precautionary management policy would pay special attention to the posssibility of its occurence. A particular feature of our simulation results is their demonstration that inappropriate combination of distinct subpopulations both increases process noise and distorts the expected stock–recruitment relation, thereby greatly reducing the accuracy of any system identification process.

Comparative experimental transmission of cardiomyopathy syndrome (CMS) in Atlantic salmon Salmo salar

Cardiomyopathy syndrome (CMS) has been recorded in wild and farmed Atlantic salmon Salmo salar. Characteristic heart lesions primarily involving the myocardium are reported in natural outbreaks with associated mortality. To date, no experimental trials have reproduced these lesions in the laboratory. The present study reports on the first successful experimental transmission of CMS in Atlantic salmon in Scotland, with full development of the histological lesions that are described for the syndrome. Tissue homogenates of CMS-infected fish indicative of mild and severe lesions from Scottish and Norwegian natural outbreaks, respectively, were injected into naïve fish, and both induced heart lesions consistent with CMS. Lesion development was earlier and progression faster in the fish group receiving the Norwegian homogenate, but equivalent in both groups by the end time point of the experiment. The study demonstrated that the reported condition for both countries is identical, as evaluated through light microscopy, and that tissue homogenates from either mild or severely affected fish contain the transmissible agent.

Ectoparasitic sea lice (Lepeophtheirus salmonis and Caligus elongatus) infestations of wild, adult, one sea-winter Atlantic salmon Salmo salar returning to Scotland

Caligid ectoparasitic copepods are major pathological pests on cultured Atlantic salmon Salmo salar L., and their population biology has been well studied in the farm environment. The ecology of caligid infestations of wild salmon is, by contrast, rather poorly understood. We monitored return migrant one sea-winter wild Atlantic salmon in Scotland annually for infestations of 2 caligids, Lepeophtheirus salmonis (Kroyer) (between 1998 and 2005) and Caligus elongatus Nordmann (between 1999 and 2005). Prevalence of L. salmonis was 100% in all years, whereas C. elongatus prevalence ranged from 90 to 100%. Abundances fluctuated markedly between years and L. salmonis mean abundance (min. to max.: 17.4 to 31.0) was significantly greater than for C. elongatus (min. to max.: 2.9 to 23.8) in all except one year. A positive association in abundance of the 2 species, for individual fish within any one year, indicates weak or absent competitive effects on abundances for individual hosts. Individual fish within any one year appeared similarly vulnerable to infestation by either species, although Taylor’s power regression showed clear differences in density-related patterns of overdispersion amongst hosts for the 2 species. Host condition factor (expressed either as Fulton’s index, K, or the relative mass index, WR) showed significant variation among years. Parasite species abundances were not, however, determined by host condition factor, and poor condition fish were no more likely to carry high infestations than were high condition fish.

Changes in prevalence of clinical infectious pancreatic necrosis among farmed Scottish Atlantic salmon, Salmo salar L. between 1990 and 2002

Infectious pancreatic necrosis virus (IPNV) induces an economically important disease that causes a pancreatic and gut-associated pathology in freshwater fish. Currently IPN is also recognised as an emerging problem for sea water cultured salmonids. This study reports clinical IPN outbreaks in farmed Atlantic salmon, Salmo salar, in Scottish marine waters among S1 and S1/2 stock, as determined by light microscopy from 1990 to 2002. The IPN diagnosis by light microscopy was supported by isolation of the causative virus in cell culture. Prevalence was calculated from the number of positive IPN cases relative to the total number of marine reared salmon examined histologically each year. Data for Scotland indicate an overall increasing trend, but with prevalence changes between years. The prevalence of IPN in post-smolt Atlantic salmon in Scotland has increased from 1.2% in 1990 to 12.5% to date. In the Shetland Isles, IPN prevalence has increased from 1995 to 1996. Prevalence of IPN for areas of Scotland other than the Shetland Isles shows little change up to 2000, but with an increasing trend thereafter. IPN mortality and histological evidence of infection was first recorded in S1/2 salmon in 1996. IPN was recorded among S1 post-smolts during the spring months several weeks after transfer to sea. Outbreaks of IPN reached a peak in July following spring seawater transfer, and clinical was IPN uncommon after October. Mortality at sites with confirmed IPN varied between 0.03% and 0.1% per day in May and 0.5% per day in July, and then declined to early spring levels. IPN in both S1 and S1/2 fish groups showed affected acinar cells with acute necrosis and pyknosis with basophilic inclusions. IPN pathology extended into the gut mucosa and necrotic areas replaced with fibrous/fatty tissue and cell sloughing in combination with increased mucous resulting in an acute, catarrhal gut exudate. Salmon pancreas disease (SPD) was diagnosed by light microscopy in 1990 with a prevalence of 11.6%, declining to zero by 2002.

Sea lice infestations on farmed Atlantic salmon in Scotland and the use of ectoparasitic treatments

A recently compiled national database on sea lice infestations on farmed Atlantic salmon, contains detailed records for the period 1996 to 2000 from over 30 commercial sites on the west...

Isolation of salmon pancreas disease virus (SPDV) from farmed Atlantic salmon, Salmo salar L., in Scotland

A toga‐like virus was recently isolated in the present authors' laboratory from Atlantic salmon during an outbreak of PD in Ireland (Nelson, McLoughlin, Rowley, Platten & McCormick 1995). When inoculated into Atlantic salmon post‐smolts, this virus, known as salmon pancreas disease virus (SPDV), caused pathological changes in the pancreas, heart and skeletal muscle which were indistinguishable from those observed in natural outbreaks of PD (McLoughlin, Nelson, Rowley, Cox & Grant 1996). In 1996 a serological survey was carried out to determine the presence and distribution of antibodies to SPDV in Irish, Scottish and Norwegian farm‐reared Atlantic salmon (McLoughlin, Rowley & Doherty 1998). The results of this survey indicated that SPDV is present in the major European salmon‐producing countries. The present paper describes the first isolation of SPDV from farm‐reared, PD‐affected Atlantic salmon in Scotland.

Three beta-lactamases isolated fromAeromonas salmonicida, including a carbapenemase not detectable by conventional methods

The beta-lactamases of seven strains of Aeromonas salmonicida subsp. achromogenes resistant to amoxicillin (MIC > 1024 mg/l) and responsible for furunculosis in farmed Atlantic salmon in Scotland were examined to establish the mechanisms of beta-lactam resistance. Separation of a cell-free extract on an isoelectric focusing gel stained with the chromogenic cephalosporin nitrocefin showed the presence of two beta-lactamases, one with a pI of 7.9 and the other with a pI of 6.0. Hydrolysis assays of cell-free extracts of these strains demonstrated carbapenemase, penicillinase and cephalosporinase activity. However, when the beta-lactamases were separated by anion exchange chromatography, the carbapenemase activity could not be retrieved in either of the peak fractions containing the separated enzymes that had been visualised by nitrocefin. Consequently, a novel carbapenemase was discovered which cannot be detected with nitrocefin.

Plasmid‐mediated antibiotic resistance in Aeromonas salmonicida isolated from Atlantic salmon, Salmo salar L., in Scotland

Abstract. Forty oxytetracycline‐resistant isolates of Aeromonas salmonicida obtained from outbreaks of furunculosis in Atlantic salmon in Scotland were tested for their susceptibility to 12 antibacterial agents. There were 10 resistance patterns with multiple resistance to two to six antibacterial agents. Transferable R‐plasmids encoding oxytetracycline resistance were demonstrated in 11 out of the 40 isolates. The resistance transferred was multiple; to oxytetracycline, streptomycin, sulphamethoxine and trimethoprim, or to oxytetracycline and one or two of these in combination. Oxytetracycline resistance was transferred in a single, large step, >250‐fold increase, and the MICs for individual transconjugants from mating populations were the same.

Assessment of the antimicrobial sensitivity of Aeromonas salmonicida isolates from farmed Atlantic salmon in Scotland

Sixty-five isolates of Aeromonas salmonicida were assessed for antimicrobial sensitivity by disc diffusion tests and the results compared with the minimum inhibitory concentration for each isolate. The results demonstrated that disc diffusion, using a standard technique, may be used to categorize isolates as sensitive or resistant provided that the corresponding minimum inhibitory concentrations are known.

Genetic protein variation in Atlantic salmon in Scotland: comparison of wild and farmed fish

Genetic variation at six enzyme loci was examined in named lines of Atlantic salmon in culture in Scotland. Twelve lines were examined in each of two years of study. Significant differences in allele frequencies were observed between the year classes of named lines and heterogeneity was present among lines in both years. Allele frequencies in farmed lines founded on fish taken from Scottish rivers or from Norwegian farmed populations differed significantly at most loci. In both cases allele frequencies differed from those in samples of wild fish taken from 18 rivers in Scotland. Most farmed lines based on the fish of single rivers also differed from wild fish in the specific rivers from which they had been derived. Genetic distances between farmed lines and their wild sources were of the same order as those between the salmon of different rivers in Scotland. No overall reduction in heterozygosity was detected in farmed lines. Most differences between the farmed lines and their wild sources appeared stochastic in origin.

Recovery of an extremely proteolytic form of Serratia liquefaciens as a pathogen of Atlantic salmon, Salmo solar, in Scotland

During 1988, heavy mortalities were observed in three discrete populations of Atlantic salmon in Scotland. From moribund and dead animals, dense pure culture growth of an extremely proteolytic bacterium was recovered, which did not correspond to the description of any of the validly described fish pathogens. The organism, which was initially considered to have characteristics intermediate between Aeromonas veronii and Serratia liquefaciens, was eventually equated with the latter, i.e. S. liquefaciens, after seeking the advice of the Centers for Disease Control, Atlanta, U.S.A. The pathogenicity mechanism appears to involve the production of proteolytic extracellular products.

Cytogenetic studies of Atlantic salmon, Salmo salar L., in Scotland

Chromosome numbers for Atlantic salmon, Salmo salar L., from ten populations in Scotland were ascertained. The majority of fish had 2n = 58, NF = 74 karyotypes, and no polymorphisms between populations were found. The findings suggest that Atlantic salmon in Scotland are cytogenetically homogeneous.

The Status of the Atlantic Salmon in Scotland.

The Status of the Atlantic Salmon in Scotland.