Simon Mackenzie

• University of Stirling

Aquaculture now provides half of all aquatic protein consumed globally—with most current and future production occurring in low- and middle-income countries (LMICs). Concerns over the availability and application of effective policies to deliver safe and sustainable future supply have the potential to hamper further development of the sector. Creat...

Introduction Net biofouling has a significant impact for the global salmon industry in the seawater grow-out stage in terms of its management. Current mitigation strategies occur primarily through the regular removal of biofouling using in situ cleaning. While in situ net cleaning is effective there is uncertainty as to whether the equipment or dis...

Ectothermic vertebrates, e.g. fish, maintain their body temperature within a specific physiological range mainly through behavioural thermoregulation. Here, we characterise the presence of daily rhythms of thermal preference in two phylogenetically distant and well-studied fish species: the zebrafish (Danio rerio), an experimental model, and the Ni...

The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that ident...

Antibiotic compounds play an important role in the control of bacteria disease outbreaks on fish farms. Yet, the impact of commercially licensed antibiotics on the diversity and composition of the gut microbiome in some farmed fish species remains unclear. The following study explored the effect of a low-level oxytetracycline treatment on the gut m...

Smoltification in salmonids occurs during spring in response to increasing photoperiod to prepare for marine life. Smoltification is associated with increased hypo-osmoregulatory ability and enhanced growth potential, mediated by growth hormone and insulin-like growth factor (IGF)-1. Rainbow trout is uniquely insensitive to the induction of smoltif...

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding...

Background Rainbow trout ( Oncorhynchus mykiss ) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated ma...

Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of...

Background In humans the stress response is known to be modulated to a great extent by psychological factors, particularly by the predictability and the perceived control that the subject has of the stressor. This psychological dimension of the stress response has also been demonstrated in animals phylogenetically closer to humans (i.e. mammals). H...

Assessment of seawater readiness of freshwater salmon smolts is a crucial husbandry step with economic implications in salmon aquaculture but current methods rely on delayed centralised enzymic activity measurement. The efficiency of a qRT-PCR assay for sodium potassium ATPase (NKA) α1a mRNA was tested in a 3-year study on 19 hatcheries across Scot...

Background: Rainbow trout (Oncorhynchus mykiss) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated mag...

Background Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome reg...

The absence of MHC class II antigen presentation and multiple pathogen recognition receptors in the Atlantic cod has not impaired its immune response however how underlying mechanisms have adapted remains largely unknown. In this study, ex vivo cod macrophages were challenged with various bacterial and viral microbe-associated molecular patterns (M...

The burden of disease is a major challenge in aquaculture production. The fish gill characterized with a large surface area and short route to the bloodstream is a major environmental interface and a significant portal of entry for pathogens. To investigate gill responses to viral infection the salmonid gill cell line RTgill-W1 was stimulated with...

The genome sequencing of Atlantic cod revealed an immune system absent of specific cell surface toll-like receptors (TLRs), major histocompatibility complex (MHC) class II, invariant chain (CD74) and the CD4 (cluster of differentiation 4) receptor. Despite the loss of these major components considered as critical to vertebrate innate and adaptive i...

We review knowledge on applications of sustained aerobic swimming as a tool to promote productivity and welfare of farmed fish species. There has been extensive interest in whether providing active species with a current to swim against can promote growth. The results are not conclusive but the studies have varied in species, life stage, swimming s...

Background: Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome re...

Background Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome reg...

Background Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome reg...

Background: Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome re...

The role of cognitive factors in triggering the stress response is well established in humans and mammals (aka cognitive appraisal theory) but very seldom studied in other vertebrate taxa. Predictability is a key factor of the cognitive evaluation of stimuli. In this study, we tested the effects of stressor predictability on behavioral, physiologic...

Individual stress coping style (reactive, intermediate and proactive) was determined in 3 groups of 120 pit tagged European seabass using the hypoxia avoidance test. The same three groups (no change in social composition) were then reared according to the standards recommended for this species. Then, 127 days later, individuals initially characteri...

The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event...

In fish, proactive and reactive individual stress copying styles (SCS) have been used to resolve variation in molecular expression data. Stress coping styles have been previously described in several stages of Solea senegalensis by validating for the species the use of standard behavioural screening tests. The present study aimed to link behavioura...

Both temperature and photoperiod affect salmonid growth and smoltification. These environmental factors are monitored or/and manipulated for the optimization of Atlantic salmon (Salmo salar) production. However, use of this strategy is limited for the smolt production of rainbow trout (Oncorhynchus mykiss), as the effects of temperature and its int...

The European sea bass is one of the most important cultured fish in Europe and has a marked sexual growth dimorphism in favor of females. It is a gonochoristic species with polygenic sex determination, where a combination between still undifferentiated genetic factors and environmental temperature determines sex ratios. The molecular mechanisms res...

A wide range of raw materials are now used routinely in aquaculture feeds throughout the world, primarily to supply protein and energy in the form of lipid from edible oils. Protein meals and oils used can generally be divided into those of plant or animal origin and many have considerable potential to supply the required dietary nutrients required...

Photoperiod is thought to be the main zeitgeber that induces smoltification in salmonids. However, its effects on the smoltification of rainbow trout (Oncorhynchus mykiss) are not fully understood and no published data documents the effects of the photoperiod regime currently used commercially, continuous light (LL). The present study compared the...

Aquaculture has grown steadily in the last few decades playing an increasing role to meet the growing demand for fish in an increasing world population. One of the biggest challenges in aquaculture is disease caused by viruses, bacteria or fungi. Among these pathogens, viruses are the most dominant agents that cause very significant aquaculture los...

Mycotoxins, secondary metabolites produced by moulds, are responsible for causing significant economic losses due to spoilage of agricultural products but also due to direct or indirect health impact on livestock upon ingestion of mycotoxin contaminated feedstuffs. Aquaculture farmed species are not an exception and studies reporting mycotoxin‐rela...

The production of seawater-transferred rainbow trout (Oncorhynchus mykiss) has recently shown an increase in production, reaching 87,000 tones in Norway alone in 2016. However, an unwanted phenotype of the species is causing major economic losses, especially during the summer season, when the problem is most prevalent. After seawater transfer, a si...

What zebrafish reveal about importance of looks vs personality in choosing a mate https://theconversation.com/what-zebrafish-reveal-about-importance-of-looks-vs-personality-in-choosing-a-mate-103611 When it comes to finding a suitable partner to raise a family, we know that our looks and the way we behave are both crucial to how well we succeed. If...

Individual differences in animal personality and external appearance such as colouration patterns have both been extensively studied separately. A significant body of research has explored many of pertinent ecological and biological aspects that can be affected by them and their impact upon fitness. Currently little is known about how both factors...

Juvenile growth at 30 dpf. Detailed significant differences in total length between personalities and colour phenotypes from 30 dpf juveniles. R WT-UAB vs P WT-UAB ***p<0.001; P WT-I vs P WT-UAB *p = 0.02; R WT-I vs P WT-UAB ***p<0.001. (TIF)

Experimental set-up of the risk-taking tank for the behavioural screening. The tank has a sheltered area (1/3 of the tank) with all sides and top covered. The open area covers 2/3 of the tank and represents a novel environment. Both sides are separated by a PVC sheet with a whole in the middle to allow the fish to cross between areas. (TIF)

Larval growth. Significant differences between colour phenotype and larval growth (p<0.001) were also observed for 21dpf larvae and juveniles (at 30dpf). *p <0.05 and **p<0.01. (TIF)

Larval growth at 21 dpf. Detailed significant differences in total length between personalities and colour phenotypes from 21 dpf larvae. R WT-UAB vs P WT-UAB ***p<0.001; P WT-I vs P WT-UAB **p = 0.002; R WT-I vs P WT-UAB ***p<0.001. (TIF)

Smoltification comprises a series of simultaneous, yet often independent, biochemical, physiological, morphological and behavioural changes that preadapt anadromous salmonids to life in seawater. This process has been extensively studied in Atlantic salmon (Salmo salar) from an endocrine, physiological and gene expression point of view. However, in...

The trend toward using plant-based ingredients in aquafeeds is set to intensify; however, mycotoxin contamination might be a chal- lenge. Two diets, with deoxynivalenol (DON) levels of 1,166 μg/kg (1.1 DON) and 2,745 μg/kg (2.7 DON), were prepared for short- term DON exposure (50 days). A third diet with a low DON level of 367 μg/kg (0.3 DON) was p...

Ectotherms choose the best thermal conditions to mount a successful immune response, a phenomenon known as behavioral fever. The cumulative evidence suggests that behavioral fever impacts positively upon lymphocyte proliferation, inflammatory cytokine expression, and other immune functions. In this study, we have explored how thermal choice during...

mRNA primer sequences used for absolute RT-qPCR analysis.

Kinetic of the behavioral fever. The table shows the frequency of chamber occupation in individual fish challenged with infectious pancreatic necrosis virus during 24 h post-infection, the video cameras provided continuous monitoring of each tank chamber. The frequency was recorded for 10 s every 15 min throughout 24 h.

Average H3K4me1, H3K4me3, 3K27me3, H3K27ac RPKM values of 5′ and 3′ sides, and flanking regions of for (A) fever genes TSS-containing domains (n = 1,726), and (B) no fever genes TSS-containing domains (n = 1,369) broader than 10 kb: infectious pancreatic necrosis virus challenged (red), control (blue).

The inflammatory reflex modulates the innate immune system, keeping in check the detrimental consequences of overstimulation. A key player controlling the inflammatory reflex is the alpha 7 acetylcholine receptor (α7nAChR). This receptor is one of the signalling molecules regulating cytokine expression in macrophages. In this study, we characterize...

The impact of deoxynivalenol (DON) on rainbow trout, Oncorhynchus mykiss, is mainly characterised by impaired growth performance and reduced feed intake, usually with the total absence of any visible clinical signs. Despite the high concentrations of DON in the present study (up to 11,412 ± 1141 μg kg⁻¹), no clinical signs (except anorexia at the h...

A fever, or increased body temperature, is a symptom of inflammation, which is a complex defence reaction of the organism to pathogenic infections. After pathogens enter the body, immune cells secrete a number of agents, the functions of which stimulate the body to develop a functional immune and fever response. In mammals it is known that PGE2is t...

Conclusions Low level of inhibition of MDP internalization by CyD both in polarized and non-polarized epithelial cells suggests MDP entry is via actin-independent mechanisms. The high level of inhibition of LPS internalization by CyD in both polarized and non-polarized epithelial cells suggest actin-dependent endocytosis.

Deoxynivalenol (DON), a Fusarium mycotoxin, is one of the most prevalent mycotoxins in aquafeeds. The toxicokinetics of DON are rarely studied in aquatic species. The present study used juvenile rainbow trout (Oncorhynchus mykiss) with a mean initial body weight of 7.72 ± 1.42 g in order to evaluate the pharmacokinetic behaviour and the metabolizat...

Dominance is defined as the preferential access to limited resources. The present study aimed to characterise dominance in a non-aggressive flatfish species, the Senegalese sole (Solea senegalensis) by 1) identifying dominance categories and associated behaviours and 2) linking dominance categories (dominant and subordinate) with the abundance of s...

Experimental tank set up used for the place preference test (with sand) in pairs. A Preferred area (sand) and B white tiles forming a false bottom characterized the novel conditions. C Water inlet. D Water outlet. (TIF)

Spearman’s correlations from the three variables “Approaches, SAA and RTH” with feeding. (**) correlation was significant P < 0.05. (TIF)

Raw data of preliminary results in dyadic pairs of early Senegalese sole juveniles. (XLSX)

Classification of the different variables in groups according to Kendall’s concordance coefficient (W) for every group. (*P < 0.05) level of significance. (DOCX)

Group experimental tank set up used for feeding response and point feed delivery. A PVC tube to deliver the food. B Water Inlet. C Water Outlet. Different position areas (1–6) were shown by point lines. (TIF)

Principal component analysis of the different behaviours registered during the “feeding response test” in pairs. The three variables “Approaches, SAA and RTH” were grouped together and explained the 53% of the variance of the data. KMO (0.667), Bartlett’s test (P < 0.05) and X2 (133.523). (TIF)

Principal component analysis of the different behaviours registered during the feeding dominance test and place preference test (sand) in pairs. The three variables “Approaches, SAA and RTH” and the “TF and last” explained the 56% of the variance of the data in two different components. KMO (0.6), Bartlett’s test (P < 0.05) and X2 (116.806) (SPSS 1...

Gill is one of the most important organs in teleost fishes which plays the central role in respiration and osmoregulation (Evans et et. al. 2005). An intact barrier is essential for the physiological activities of the tissue. However, the barrier is not static, can be modulated by specific insults like environment, pathogens, toxins (Benson et al....

An immunostimulant (IS) is a natural or chemical substance that stimulates the immune system by specific (vaccines or antigens) or non-specific (irrespective of antigenic specificity) routes. This chapter provides some insight into the target tissue of many IS diets; the fish mucosa. The use of IS-containing diets in aquaculture is widespread and e...

This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a larg...

Recent advancements within state-of-the-art genomic tools and the generation of the first version of the Atlantic cod genome (Star et al., 2011) have proven to be valuable resources, improving our understanding of this species’ biology. In this chapter we describe some aspects and implications of using these resources to identify genes and molecula...

From the excellent contributions throughout this book it has become very apparent how genomics-driven research is impacting upon aquaculture. Moving through the chapters from the cutting edge technologies developed in the zebrafish to their translational application highlighted, for example, in the turbot exemplify how genomics is shaping fish biol...

Genomics in Aquaculture is a concise, must-have reference that describes current advances within the field of genomics and their applications to aquaculture. Written in an accessible manner for anyone-non-specialists to experts alike-this book provides in-depth coverage of genomics spanning from genome sequencing, to transcriptomics and proteomics....

First steps towards biomarker discovery in salmonids using MALDI-TOF MS with special emphasis on the methods used

In this study, we aimed to analyze the global response to iron in the broad-range host pathogen Vibrio vulnificus under the hypothesis that iron is one of the main signals triggering survival mechanisms both inside and outside its hosts. To this end, we selected a strain from the main zoonotic clonal-complex, obtained a mutant in the ferric-uptaker...

Environmental temperature gradients provide habitat structure in which fish orientate and individual thermal choice may reflect an essential integrated response to the environment. The use of subtle thermal gradients likely impacts upon specific physiological and behavioural processes reflected as a suite of traits described by animal personality....

Abstract for a presentation on the FITFISH COST action annual conference in Belgrade, April 2016

Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with h...

The question of whether animals other than humans can think and feel has been debated for centuries. Most of us would agree that humans have a level of consciousness, loosely defined as an ability to experience thoughts and emotions. But which other creatures have consciousness remains an open and controversial question.

Common carp Cyprinus carpio displaying proactive or reactive stress coping styles were acclimated to two environmental regimes (low oxygen and low temperature), and selected groups were tested for response to an inflammatory challenge (Escherichia coli lipopolysaccharide, LPS). Plasma glucose and lactate levels were measured, as were selected C. ca...

Whether fishes are sentient beings remains an unresolved and controversial question. Among characteristics thought to reflect a low level of sentience in fishes is an inability to show stress-induced hyperthermia (SIH), a transient rise in body temperature shown in response to a variety of stressors. This is a real fever response, so is often refer...

Whether fish are sentient beings remains an unresolved and controversial question. Among characteristics thought to reflect a low level of sentience in fish is an inability to show stress-induced hyperthermia (SIH), or emotional fever, a transient rise in body temperature shown in response to a variety of stressors. It has been suggested that the c...

Infectious diseases are one of the principal bottlenecks for the European eel recovery. The aim of this study was to develop a new molecular tool to be used in host-pathogen interaction experiments in the eel. To this end, we first stimulated adult eels with different pathogen-associated molecular patterns (PAMPs), extracted RNA from the immune-rel...

The alpha7nicotinic acetylcholine receptor (alpha7nAChR) is present in different cells of the immune system such as macrophages and lymphocytes and, in mammals, has been shown to be essential for controlling inflammation in response to LPS. This homeostatic system is known as inflammatory reflex and involves the activation of splenic lymphocytes an...

It has been widely supported that individual animals express different strategies to cope with environmental challenge. In ectothermic species such as fish, individuals must use behavioral thermoregulation mechanisms to optimize physiological performance. In the present study, thermal preference was tested in groups of wild-type zebrafish, Danio re...

The COPEwell project aims is to develop a new integrative framework for the study of fish welfare based on the concepts of allostasis, appraisal and coping styles. The project focuses on the understanding of how fish experience their world, and what effects early life experiences have on later development and coping abilities.

Resolving phenotype variation within a population in response to environmental perturbation is central to understanding biological adaptation. Relating meaningful adaptive changes at the level of the transcriptome requires the identification of processes that have a functional significance for the individual. This remains a major objective toward u...

Abstract Septic shock is the most common cause of death in intensive care units due to an aggressive inflammatory response that leads to multiple organ failure. However, a lipopolysaccharide (LPS) tolerance phenomenon (a nonreaction to LPS), is also often described. Neither the inflammatory response nor the tolerance is completely understood. In th...

It has not been elucidated whether or not autophagy is induced by rhabdoviral G glycoproteins (G) in vertebrate organisms for which rhabdovirus infection is lethal. Our work provides the first evidence that both mammalian (vesicular stomatitis virus, VSV) and fish (viral hemorrhagic septicemia virus, VHSV, and spring viremia carp virus, SVCV) rhabd...

Skin integrity is recognized as of vital consideration for both animal welfare and final product quality of farmed fish. This study examines the effects of three different rearing temperatures (4, 10 and 16 °C) on the skin of healthy Atlantic salmon post-smolts. Changes in skin condition were assessed by the means of skin composition analyses, quan...