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Promoting excellence

Promoting excellence

Stirling’s research

- shaping the future of global aquaculture Stirling Front Cover.indd 1

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Contents 3 4-7 8-9 10-11 12-14 15 16-18 19 20-21 22-23 24-25 26-29 30-31 32 33 34-36 37 38-39 40-41 42-44 45 46-47 48-51 52-53 54 55 56 57 58-59 60-62 63 64-65 66-67 68 69 70-71 72-73 74-75 76-77 2

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Introduction PhD conference Parliamentary inquiry Scottish Aquaculture Innovation Centre Douglas Tocher Xu Gong Monica Betancor IFFO, the Marine Ingredients Organisation David Pond Oscar Monroig Scottish Sea Farms John Taylor Yehwa Jin Michael Clarkson Michael McGowan Marine Harvest Scotland Bernat Morro Luisa Vera Lewis Warren Scottish Salmon Company AGD Armin Sturm Herve Migaud Rowena Hoare Ahmed Elkesh Andrew Desbois 20 Shankar Manda Sean Monaghan Chris Payne Grieg Seafood Steve Prescott Lynne Falconer WorldFish 72 Trevor Telfer Dimitar Taskov William Clark Dave Little Francis Murray Dave Little

78 79 80-81 82 83 84-85

Sonia Rey Manfred Weidman Suleiman Isa Khalid Shahim Isah Lawal Global Aquaculture Alliance Will Leschen 86 Susan Fitzer 87 Philip Graham 88 Francis Murray 89 Stefano Carboni 90 Simao Zacarias 91 92-93 Facilities 94-95 CPD 96-97 AKVA Group Brendan McAndrew 98 Sponsors 99



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Stirling’s research, shaping the future of global aquaculture THE Institute of Aquaculture, founded in 1971, is an international centre for world-class research and teaching. As a catalyst for innovation and enterprise, it provides a global hub for the creation of sustained research partnerships across the aquaculture community. The Institute brings together cross-disciplinary, world class researchers to meet the wide range of challenges faced as aquaculture grows to meet global demand. Our research focuses on critical questions relating to strategies for sustainable aquaculture and aquatic food security, whether in modern commercial markets or in supporting communities in developing countries. The Institute offers expertise, training and development of innovative technologies, new techniques and state-of-the-art practices relating to the sustainable farming of aquatic products for human use. Our capacity extends to understanding the roles of aquaculture within societies, its governance and interface with broader food systems. Fundamental and applied research on reproduction, genetics, genomics, aquatic animal health and welfare, nutrition, production systems, environments, markets, and social and economic impacts all play significant roles. The Institute uses this wide research base to focus on addressing the key challenges facing producers, consumers, retailers, regulators and policy makers of the world’s most important aquaculture industries. It is dedicated to supporting the development of global sustainable aquaculture production to address future protein production requirements in the context of social, economic and environmental change. We attract research funding from a wide range of sponsors, including the Scottish Funding Council, UK Research Councils, UK government departments, the European Union, national and international research organisations, foundations, trusts and industry. We have collaborative research and training partnerships and links with many other academic institutions throughout Europe and further afield. Importantly, the Institute provides a range

of training and teaching courses relevant to aquaculture and aquatic science. The Institute has a strong and successful history in the provision of a Master in Sustainable Aquaculture with more than 1,000 alumni since its inception. Building on the Institute’s long standing reputation, we are broadening our provision of education and training. Working with partners across Scotland and internationally, the Institute is offering a range of flexible learning courses through a number of routes, with several exit points, including CPD and bespoke courses. This special issue summarises the range of research and teaching activities performed at the Institute and showcases some of the most innovative research projects currently ongoing to tackle industry challenges and knowledge gaps. It is a strong testimony to the excellent, impactful aquaculture research being performed at Stirling. This is only possible due to the large and multinational group of researchers, technical support staff and PhD students based at the Institute, whose contribution to ongoing research and vibrant research culture is greatly valued. And we also benefit from strong partnerships with industry players, several of whom have sponsored this publication. I’d like to thank Denny Conway for his help and all colleagues and students at the Institute of Aquaculture for sharing their research interests, knowledge and pictures. If you wish to obtain further information on a specific project, research area or training course, please contact the scientists involved directly, via or alternatively catch them at Aquaculture UK in Aviemore in May or the EAS/WAS conference in Montpellier in August. We hope that you enjoy the read. Prof. Herve Migaud Editor Chair in Fish Breeding and Stock Improvement

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Next generation Students present cutting edge science at PhD conference DISEASE outbreaks in cleaner fish, autogenous vaccine development, the role of hyper-parasites in complex gill disease, and the dietary requirements of African catfish were just some of the topics discussed by students at the fifth PhD conference in Stirling on April 17. Some 37 current students either gave talks or displayed posters at the event, on subjects ranging from hatchery practices in the Nigerian aquaculture industry and emerging bacterial disease in Nile tilapia, to the development of triploid Atlantic salmon and the effects of temperature and diets on rearing ballan wrasse. Following a keynote talk from Dr Iain Berrill of the Scottish Salmon Producers Organisation, Michael McGowan presented the results of a three-year study to uncover the secrets of smoltification in Atlantic salmon. ‘Due to their anadromous lifecycle, transfer of salmon from fresh water to seawater post smoltification is crucial,’ said McGowan. ‘Early transfer can cause mortality through sub-optimal adaption of their physiology and morphology to the seawater conditions and promote susceptibility to viral infection. Late transfer can lead to de-smoltification and long-term detrimental health problems.’ Currently, only laboratory based detection platforms to monitor smoltification are available to definitively indicate when smoltification is occurring in salmon. McGowan said that a mobile assay was developed


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that has the potential to be used as a future biomarker for detection of smoltification both in lab and onsite. ‘Successful application of the mobile platform on site opens the possibility to add further smoltification transcript assays to increase the robustness of the test and also the addition of viral transcripts for onsite virus detection.’ Examining one of the major health problems in Atlantic salmon, Ana Herrero looked at the role of the microsporidian parasite Desmozoon lepeophtherii in complex gill disease (CGD). ‘Studies have demonstrated that parasite densities are significantly higher in fish suffering from gill disease,’ said Herrero, ‘but despite the parasite having been shown to be detrimental to farmed Atlantic salmon, the exact role it plays is still unknown due to the difficulty in detecting the parasite under light microscopy.’ A novel in situ hybridisation method using a DNA probe allowed the detection of the D. lepeophtherii and helped to clarify its role in CGD.

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Next generation

Opposite page: Students at the PhD conference. Above: The Institute of Aquaculture’s PhD students. Right: Prof Sandra Adams offers advice

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One of the poster presentations also focused on gill disease in salmon. Carolina Fernandez compared different swabbing methods for optimised diagnosis of amoebic gill disease (AGD). ‘As the accuracy and sensitivity of this diagnostic method is critical to timely treatment in a commercial situation, the type of swab material should be optimised to ensure not only efficient sample capture but also maximum recovery of the sample organism to be subsequently analysed and quantified,’ said Fernandez. Another poster focused on the search for a recombinant vaccine against AGD. Jadwiga Sokolowska outlined the aims of the study, funded as part of the EU ParaFishControl project. The results will facilitate further stages of vaccine development that will focus on identification of immunogenic proteins as potential vaccine candidates. Michael Clarkson talked about reducing the health problems associated with triploidy (rendering fish sterile) which, he said, has the potential to play an important role in the developing aquaculture industry. Sterile fish can combat escapees interbreeding with wild populations and also have potential for increased growth as energy reserves would be redistributed. Triploid salmon have previously been associated with inferior growth and skeletal malformations, and this research investigated egg incubation temperatures, thought to be of particular importance as triploids

Be flexible, keep your mind open to opportunities and to your own skills…and never stop learning

are believed to be more thermosensitive than diploids and embryogenesis is an important developmental onset. However, reducing egg incubation temperatures will slow development and may be problematic for a commercial production cycle. The aims of the trial are to identify a more specific life stage where development of negative characteristics begins, investigate whether incubation under a particular temperature is only required for a short period to control the impact on freshwater production duration, and establish biomarkers for early indication of these issues. Two PhD students delivered talks on ballan wrasse, with Athina Papadopoulou looking at the development of a vaccine against atypical Aeromonas salmonicida, a common disease affecting the species. 5

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seabream in the same production sites Two studies on Nile tilapia were presented, the first by Khalid Shahin, whose research centred on francisellosis, an emerging bacterial disease representing a major threat to the global tilapia industry. The study aimed to evaluate the efficacy of an autogenous injectable vaccine against homologous and heterologous isolates, and found that vaccinated fish had significantly higher relative per cent survival than adjuvant-injected and control fish. This whole-cell inactivated vaccine provides the basis for developing a broad spectrum, highly protective vaccine against emerging francisellosis outbreaks, said Shahin. Ye Hwa Jin, meanwhile, talked about developing an alternative sterility method in fish. The rationale for the research was to enhance the current understanding of primordial germ cells (PGCs) and gonadal development in Nile tilapia, and then to explore the viability of gene editing to induce sterility. The research team was able to identify a gene that plays an important role in the survival of PGCs in early larval stage in Nile tilapia, the first demonstration of such gene editing, resulting in putative sterile fish in a commercially important farmed species. Angela Oboh and Suleiman Isa investigated catfish culture, exploring, respectively, biosynthesis of longchain polyunsaturated fatty acid (LC-PUFA) in the species, and current hatchery practices in Nigeria’s catfish sector. Oboh said studies have shown that the potential of a species for LC-PUFA biosynthesis is associated with very long chain fatty acid genes existing in that species. Even within closely related species the complement of these genes and their functionalities can vary remarkably, underscoring the need for studies on each individual farmed fish species. Her study confirmed that African catfish possess all the enzymatic capabilities required for the biosynthesis of physiologically important compounds, including arachidonic acid (ARA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and, therefore, its essential fatty acid requirements can be satisfied with dietary provision of long chain polyunsaturated fatty acid. Suleiman Isa, a Commonwealth Scholar, part funded by the UK Commonwealth Scholarship Commission, explained the contribution of farmed catfish to Nigeria’s growing aquaculture industry. Until recently, most studies on the aquaculture of this species had been based on the nutrition, physiology

Above: Iain Berrill (SSPO) Sandra Adams (IoA), Giuseppe Paladini (IoA), host Vivienne Parry, and IoA interim director Maggie Cusack. Left: MSc student Tarah Mayes. Opposite page: The poster display.

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Next generation and culture systems, with little known on the genetics and genetic management of the different populations of wild and cultured African catfish (Clarias gariepinus) within and between different countries. In his presentation, he described how a survey of hatcheries and farms in Nigeria was carried out as a prerequisite for setting up a selective breeding programme to improve growth rate, survival, and reduce inbreeding depression, cannibalism, poor quality of fingerlings and uneven growth currently reported in the industry. Shankar Chandra Mandal, who also received Commonwealth Scholarship Commission funding, gave a talk on the response in trout to salmonid alphavirus subtypes, associated with sleeping disease of rainbow trout in freshwater aquaculture. And Bernat Moro’s study provided the first dataset of protein markers for smoltification and seawater adaptation, which will be used to understand the changes in the proteome during these processes and to identify biomarkers. In A.H.Junaidi’s research, lipid homeostasis in farmed fish was studied, with the ultimate aim of improving finfish feed formulation to better optimise the relationship between lipid input, fat accumulation and growth.

Learn how to be good communicators YOUNG scientists need to communicate their research to a wider audience, students were told at the Institute of Aquaculture’s PhD conference as they showcased the results of several years’ study in front of their teachers, peers, and industry guests. ‘You should know how to say your PhD in one phrase in case you’re stuck in the lift with the head of the department,’ said the broadcaster Vivienne Parry, the host for the day. Then, hopefully, they will say, ‘that’s interesting, please tell me more’. Professor Sandra Adams, one of three keynote speakers, also emphasised to the postgraduate community the importance of being able to explain their work to people who were not specialists. The Institute of Aquaculture is proud of its large and international body of research students, currently numbered at 75, and says their ‘enthusiasm and energy are among the most stimulating aspects of academic life’. These ‘researchers in training’ are provided with an excellent framework at the university to apply their science, with many funded, at least in part, by the industry, and they were offered advice on where their efforts could lead them. Professor Adams, head of the Aquatic Vaccine Unit, talked about the benefits of a career in academia, pointing out that it’s not all about working in a lab. One of the highlights of her job, she said, was travelling. ‘Take opportunities when they crop up… and network and be visible,’ she said. She attributed her rise in academia to being in ‘the right place at the right time’, when salmon farming was just taking off in Scot-

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land in the 1980s and there were bacterial disease problems. ‘There was an urgent need for fish vaccines to prevent disease and reduce the use of antibiotics.’ She was attracted to aquaculture because she could apply her knowledge and help the industry, but could also do fundamental science too – and travel. Her advice to students wishing to follow the academic path was to get experience in other areas because the jump from post-doctoral research to full-time lecturer was a big one, and researchers may have to work on three to four post-doc projects before promotion. ‘Success doesn’t find you, you have to go out and get it.’ Living proof of this maxim was Dr Iain Berrill, technical manager of the Scottish Salmon Producers Organisation (SSPO), who said he did his MSc in Plymouth because he couldn’t get on to the very popular course in Stirling. ‘But Stirling came to its senses and I was able to come back and do my PhD here,’ he said, although things didn’t always go smoothly. Part funded by Marine Harvest, he was looking into the precocious maturation of salmon parr, but in 50% of his experiments the fish failed to mature and by the time he had finished his research, the industry had solved the problem itself. Undertaking an industrial PhD taught him valuable lessons, though, he said. One was that the industry moves very quickly to solve its problems, and another is that your brilliant piece of work might not be very useful in the end.

The message to students was not to be constrained by the subject of their doctoral research – and that academic qualifications are only part of what is needed. Berrill stressed the importance of working up through the ranks and said the industry really needs to get people from academic backgrounds on to farms to teach them about fish farming. His contemporaries from Stirling have moved into a variety of roles – from academia, to the head of a pharmaceutical company, the CEO of a Tasmanian salmon company, and the communications manager of Oxfam. ‘So be flexible, keep your mind open to opportunities and to your own skills…and never stop learning.’ Heather Jones, CEO of the Scottish Aquaculture Innovation Centre, gave the PhD students further careers advice: ‘Don’t be afraid to use the connections you’ve made, ask for help (‘phone a friend’) – and make yourself useful by thinking about things from others’ point of view.’


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Scientists shine new light on salmon farming Professors provide timely advice to MSPs during parliamentary inquiry SCIENTISTS from the Institute of Aquaculture were part of a panel of experts giving evidence to the Rural Economy and Connectivity (REC) committee’s inquiry into Scottish salmon farming in March. They were the first to appear in a series of sessions which concluded on May 9 with the Cabinet Secretary for the Rural Economy and Connectivity, Fergus Ewing, answering MSPs’ questions. The Holyrood inquiry was set up following a petition from interests in the angling sector, and has heard from members of the wild fishing lobby, government regulators, conservation bodies, representatives from Scotland’s food and drink sector, and salmon producers. It is now considering its recommendations, which will be published in a report, possibly before the parliamentary summer recess. Professors Herve Migaud and James Bron, both of Stirling’s Institute of Aquaculture, took part in the session on March 7, along with Professor Paul Tett, reader in Coastal Ecosystems, from the Scottish Association for Marine Science (SAMS), and economist Steve Westbrook. Below is a report of the committee’s hearing as reported in Fish Farmer.

longer period. But it’s more difficult to treat sea lice because of gill health problems, and the industry has been in a transition period, moving from veterinary medicines to relying on a different approach, involving different tools. ‘We’ve had to learn how to deal with these problems but the industry has learnt how to cope with those.’ Putting farmed salmon mortalities (around 20 per cent last year) into context, Migaud, Professor of Aquatic Breeding and Physiology, said salmon mortality in the wild is about 90 per cent. ‘In some cases it’s 70 per cent, but it’s up to 99 per cent most of time. That doesn’t justify what’s in farmed but that’s the biology.’ In most important finfish species, mortality rates are high. The lowest mortality is in sea bass and bream, which has up to 45 per cent survival, but cod survival is lower than 10 per cent. As for the causes of wild salmon mortality, Bron said unless dead fish wash up on beaches it is hard to tell how they died. The ocean is a ‘black box’ and very difficult to access. ‘Even without fish farming, wild fish can have 70 per cent infected with sea lice, without impacting their health. So working out the effect on wild fish is very hard to do. ‘We’re farming something not far from a wild fish, so they tend to have the same diseases. The potential for introducing diseases to the wild population is therefore low.’ Farmed salmon are not fed ‘unprocessed trash fish, introducing pathogens’, and there are very good controls on the movement of salmon. The launch of the REC committee’s inquiry follows the conclusion of an invesThe numbers of sea lice on Scotland’s salmon tigation into salmon farming’s environmental impact, conducted by the Environfarms are not increasing, farmers have better control ment, Climate Change and Land Reform (ECCLR) committee. of parasites today than in the past, and the risk of It released its findings at the beginning of March, criticising the industry’s endisease transfer from farmed to wild fish is low. vironmental performance, and warning that Scotland’s marine ecosystem faces A very different picture of the state of Scotland’s ‘irrecoverable damage’ from salmon farming if concerns are not addressed. salmon industry emerged when leading fish health The ECCLR probe was informed by a report produced by SAMS, but Tett, one experts appeared before Holyrood’s new inquiry into of the authors of the report, conceded to the REC inquiry that ‘our report may the sector. not be completely up to date’ because it was based on a review of existing Asked by Richard Lyle, SNP MSP for Uddingston literature. and Bellshill, about recent high mortality rates at Also, much of the information in the review was derived from Norwegian salmon farms, Prof Bron said there was a diverse data but, as Tett, Migaud and Bron all pointed out, the two countries have range of health challenges at the moment. some significant differences. ‘The impression is that we’re getting a lot more Norway’s fjords, for instance, are deeper than Scotland’s lochs, weather is sea lice, but if you look at actual figures, numbers colder –especially in the north, and the scale of farming is much bigger. of sea lice are not increasing. Many farms may have Migaud said that Norway has an extended coastline and there are a lot of no problems with sea lice, some sites have serious local differences between the north and south – ‘we can’t apply what happens problems; mostly, sea lice are under control in Scot- there directly to Scotland’. land…the average has remained relatively static. The number of escapees entering rivers is also much higher in Norway than it ‘To manage to stay on top of that is quite a feat. is in Scotland, said Bron. The industry has not sat back,’ he said, noting that Fulton Macgregor, SNP MSP for Coatbridge and Chryston, was concerned there had been more innovation in treatments in the about resistance to antibiotics and asked the panel how widespread their use last five years than there had been across a much was in Scotland. 8

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Bron said ‘tiny… we use almost none’, and far less than other salmon farming countries, such as Chile, because of the development of very effective vaccines. The academics were also able to reassure MSPs on the subject of stocking densities, when Richard Lyle suggested less density would be better for fish mortality. Densities in the early days of salmon farming had been higher, said Bron, but ‘work we did established cut-off points for where health and welfare might suffer, so farmers all use lower density, and I think it’s about right.’ Migaud said current densities were 15kg per cubic metre for salmon, but explained to the committee that it was a challenge to get the fish to use their space better – ‘they are not fish that like to swim in isolation, they tend to congregate together’. Conservative MSP for North East Scotland Peter Chapman asked how effective cleaner fish were, while committee convenor Edward Mountain (Conservative, Highlands and Islands) wondered if there was a market for wrasse and lumpsuckers, once farmers had finished with them. Migaud agreed that was a very important consideration and that the industry was already looking into it. There was a potential export market for wrasse in Asia, while chefs around the world were trying to be innovative in finding uses for lumpfish – ‘but we’re still not there’. However, greater progress was being made in farming cleaner fish. There were challenges regarding the robustness of the fish before deployment, but ‘we’re prototyping vaccines at present’, said Migaud. The majority of cleaner fish are now farmed and in a couple of years the industry would be fully supplied by farmed lumpfish and wrasse. This was one example of good collaboration between the industry and academia, but there were

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Above: Professor Paul Tett, Professor James Bron, Professor Herve Migaud and Steve Westbrook at the inquiry

plenty more, with ‘fantastic innovations’, many appearing in the last five years and so still bedding down, said Migaud. These included the use of recirculation hatcheries to reduce the time fish spent in open cages, optical delousing, functional feeds to boost mucus production and reduce sea lice attachment, and well-boats with reverse osmosis, capable of producing freshwater. If there were knowledge gaps in the Scottish industry they were being addressed. The convenor asked all panel members if they believed the target to double growth by 2030 could be achieved without detriment to the environment. Tett said yes, ‘but there will need to be radical changes in the way farming is managed and regulated’, while Migaud said ‘it has to be done sustainably to meet this growth’, and Bron noted that problems needed to be solved, but the industry was working hard. Steve Westbrook, author of a report on the value of aquaculture to Scotland, thought 50 per cent growth was much more likely than 100 per cent, even if everything was favourable, and getting to 300,000 tonnes was more likely than 400,000 tonnes. But if the technology could generate more farms in offshore sites to get larger volumes, and there was less need to operate inshore sites, ‘a lot of the issues discussed will fade away’.

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Supporting research - Scottish Aquaculture Innovation Centre

Match making SAIC helps connect industry and academia to address challenges IT’S an exciting time to be part of Scottish aquaculture. Populated by passionate and hard working people, this is a sector that not only recognises the need and scope for innovation, but shows a genuine commitment to developing sustainable solutions to the industry’s challenges. Since 2014, the Scottish Aquaculture Innovation Centre (SAIC) has been the connecting force in coordinating industry and academia to address these challenges. SAIC works with 75 industry partners and 20 research organisations to accelerate innovation, strengthen national food security and support environmental stewardship. So far, SAIC has facilitated more than 20 collaborative projects, with a combined investment of £34 million – creating the right environment for innovation.

Making investment work harder SAIC works with industry and academia to make sure that innovation is directed to where it is needed the most, and that investment into essential research and development generates measurable return. For each £1 of government support for core industry-academic collaboration projects, SAIC has attracted £5.19 of investment from industry and other funding sources. Launching vital new research In April, SAIC launched a two-year collaborative project to help accelerate understanding of gill health issues in farmed salmon and identify new approaches to overcoming these issues. Co-funded by SAIC and valued at almost £800,000, the project team combines expertise in feed manufacturing (BioMar) and salmon farming (Scottish Sea Farms) with world leading fish health expertise at the University of Aberdeen, supported by Marine Scotland Science. Creating a pipeline of talent People are key to success in any business, and one of SAIC’s goals is to help close aquaculture’s skills gap. The centre is keen to promote the diverse and rewarding careers available in the sector. It has de10

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Match making

signed and implemented an aquaculture graduate development programme, which aims to create a talent pipeline of industry leaders. SAIC’s skills initiatives also include industry placed internships, postgraduate conference grants, and funding for MSc places. Engaging with stakeholders SAIC collaborates with a consortium of nearly 100 businesses, academic institutions and other stakeholders. From Shetland to Stirling and from Machrihanish to Madrid, it engages with colleagues in the aquaculture sector through collaborative projects, meetings and events. To help share knowledge and drive innovation, SAIC’s Connect + Collaborate programme has encompassed more than 1,250 industry engagements to date. Showcasing industry ambition A recent collaborative bid to secure £100 million R&D support from the UK Industrial Strategy Challenge Fund is an exciting step for the sector.

We are keen to promote the diverse and rewarding careers available in the sector

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Universities and industry have joined together to bid for funding to improve fish health and boost the contribution aquaculture makes to the economy. If successful, the research aims to increase productivity by £66.5 million a year, increase exports by 10.5 per cent, decrease farmed fish mortality by 50 per cent and deliver a five per cent reduction in the carbon footprint by 2025. To find out more about SAIC, visit

Clockwise from top: SAIC CEO Heather Jones with young talent; Tom Ashton of Xelect in SAIC funded research; mussel hatchery project; SAIC at Scottish Sea Farms facility; cleaner fish summit.


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Giving salmon their five-a-day Formulating feeds for the future with alternative diets By Douglas R Tocher Above: Some of the ARRAINA crew (from left to right): Luisa Vera Andujar (UoS), John Taylor (UoS), Davie Corrigan (MH), Eva Mykkeltvedt (NIFES), Bente Torstensen (then NIFES), Chris Metochis (UoS).


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THE European Union Framework Programme 7 project, ARRAINA (Advanced Research Initiatives for Nutrition and Aquaculture) was a five-year, â‚Ź8 million project involving a multi-disciplinary consortium of 21 partners. Carried out from January 2012 to December 2016, the key objectives of ARRAINA included: to define and provide complete data on the quantitative nutrient requirements of five European aquaculture species (Atlantic salmon, rainbow trout, gilthead seabream, European seabass and common carp); to develop sustainable alternative feeds tailored to the requirements of these species with reduced levels of fishmeal (FM) and fish oil (FO); and to undertake long-term studies with fish fed alternative feeds and ensure growth, health, reproductive performance, nutritional and environmental quality.

The Institute of Aquaculture and the National Institute of Nutrition and Seafood Research (NIFES, now IMR) collaborated closely in the research on Atlantic salmon. Specifically, the IoA focused on three major nutritional trials to define dietary phospholipid requirements, validate revised micronutrient requirements in a full lifecycle trial, and to test the concept of nutritional programming in salmon. The work was led by Prof Douglas Tocher, supported by Dr John Taylor and Prof Herve Migaud, with an excellent team of post-doctoral researchers - Drs Luisa Vera, Greta Carmona, Laura Martinez, Christian DeSantis and Chris Metochis - and PhD student Mikey Clarkson. To determine phospholpid requirement in Atlantic salmon, fry were fed from first feeding with diets Institute of Aquaculture

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Giving salmon their five-a-day

salmon larvae/fry is immature and unable to synthesise phospholipid de novo, which limits lipoprotein assembly in the gut, impairing dietary fat export that can be restored by providing PC in the diet. Many micronutrient requirements reported for salmon had not been empirically determined, rather being extrapolated from data obtained with rainbow trout (National Research Council (NRC), 2011. Nutrient Requirements of Fish and Shrimp. National Academic Press, Washington DC). The development of sustainable feeds has exacerbated this situation because the composition of micronutrients is different in plant and marine ingredients and containing graded levels (1-4% of diet) of phospholipid supplied by marine (krill oil) or terrestrial (soybean the matrix of the feed may also affect the bioavailabillecithin) sources and fish sampled at 0.2, 0.5, 1, 2.5, 5, ity and metabolism of these nutrients and, therefore, 10 and 50g. Based on both growth and development, micronutrient requirements. In ARRAINA, an entirely novel screening approach Atlantic salmon were confirmed to have a requirement for dietary phospholipid, specifically about 0.3 – 0.4% was used by NIFES in two short-term trials carried out in Norway in freshwater and seawater to investigate phosphatidylcholine (PC), for optimal growth in early graded supplementation of a nutrient package based life stages up to around 2.5g, but fish of 10g showed on NRC (2011), and using micronutrient biomarkers to no requirement. Dietary phospholipid also abolished the intestinal fat determine requirement level. These revised levels were then tested and validated accumulation and decreased the vertebral deformity in Scotland by the Institute of Aquaculture in a longobserved in fish fed low phospholipid. term, full lifecycle trial in salmon fed diets formulated Regarding the mechanism underpinning this with low FM and FO. requirement, our hypothesis was that phospholipid The freshwater phase was carried out at the Neil requirement reflected immaturity of intestine in early Bromage Freshwater Research Facility, Buckieburn, life stages of fish. To test this, we compared gene expression in intestine and liver at two time points, 2g contained both diploid and triploid salmon, and con(when dietary phospholipid was required) and 10g (no tinued in seawater with the transfer of smolts (diploids only) to the Marine Harvest Feed Trial Unit, Ardnish. It requirement for dietary phospholipid). terminated a year later when post-smolts achieved a We investigated a suite of 40 genes covering all the final weight of 3.0 – 3.5kg. steps in phospholipid biosynthesis and found that Briefly, Atlantic salmon parr (~ 20 g) were initially fed around a dozen key genes involved in the biosynthesis a standard reference diet (S diet) based on commercial of PC showed low expression in intestine of 2g fish. formulations containing 30% FM/15% FO, or a low The data confirmed that the intestine of Atlantic

Nutrient requirements of triploid salmon in freshwater were greater than those for diploid salmon

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Above: Another beautiful day at Ardnish.


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“ marine ingredient formulation (L diets) containing 15% FM/8% FO supplemented with a micronutrient package (NP, NIFES modified NRC 2011 recommendations) at three inclusion levels. Therefore, the four feeds were S, 1xNP; L1, 1xNP; L2, 2xNP; L3, 4xNP. Throughout the freshwater and seawater phases, the FM/FO levels were progressively reduced with increased body and pellet size, with the final levels being 5% FM/3% FO, fed from around 2kg until the end of the trial. In freshwater, diploid salmon parr fed diets with 15% FM/8% FO required a micronutrient package with 2xNP to maintain growth at the same levels as fish fed the higher levels of FM and FO (30% and 15%, respectively). In seawater, further reduction of FM and FO down to 5% and 3%, respectively, and higher growth rates, required further increment in micronutrient package of between 2xNP and 4xNP to maintain growth at the same level as fish fed the higher levels of FM/FO. Nutrient requirements of triploid salmon in freshwater were greater than those for diploid salmon, with 4xNP levels required to maintain growth in diets fed low FM and FO suggesting higher nutrient requirements for triploid salmon. In contrast to growth, requirements for optimal skeletal health in salmon fed low FM/FO in both freshwater and seawater phases required 4xNP. These effects appeared to be mediated through altered phosphorous-calcium homeostasis pathways and subsequent mineralisation of the skeletal column, with candidate limiting micronutrients being vitamins D3 and K, key co-factors/co-enzymes in calcium sequestering, rather than the micro-minerals themselves. Salmon fed low marine diets with 4xNP values showed increased innate immune responses and reduced inflammatory responses, which could offer robustness against disease compared to salmon fed low marine diets with only 1xNP. Recommendations for nutrient requirements of Atlantic salmon fed diets with low levels of FM and FO and high inclusion of plant ingredients were provided in detail in the ARRAINA Second Technical Booklet 2016 Aquaculture Nutrient Requirements (, with many of them being 14

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Above: Bente and John hard at work.

Dietary influences exerted at critical development stages in early life may have long-term consequences


different from the values reported in NRC (2011). For nutrients that showed a satiable uptake, maximum tissue levels were used as biomarkers and, with vitamin B6, tissue levels correlated very well with the activity of the indicator enzyme, aspartate aminotransferase, supporting this approach as a valid method for the water-soluble vitamins. In contrast, nutrients that do not show a satiable uptake, such as fat-soluble vitamins, could not be fully evaluated and so require further research. Specific care should also be taken with regard to recommendations for minerals, which can be toxic in high concentrations. For instance, some evidence suggested that zinc requirements may be much higher than reported by NRC (2011) but, at the same time, zinc in high concentration can be toxic. While detailed analyses and interpretation of the data from the long-term trial are still ongoing, preliminary findings confirm that a few revisions of the recommendations for salmon may be necessary. Specifically, vitamins B3, B5 and B6 levels appeared to be sub-optimal and requirement levels are actually higher than reported in the NRC recommendations and therefore they should be increased. In contrast, levels of vitamins B1, B7, B9 and B12 appear to be sufficient at NRC levels and so no changes are recommended. The final trial carried out at the Institute of Aquaculture in the ARRAINA project was the first study of the phenomenon of nutritional programming in Atlantic salmon. The concept is that dietary influences exerted at critical developmental stages in early life may have long-term consequences on physiological functions in later life. We demonstrated that exposing salmon for a short time at first feeding to a diet with very low levels of the critical omega-3 fatty acids, EPA and DHA, enhanced their metabolism and retention when fish were fed a similar low marine diet later in life. This trial has already been the subject of an article in Fish Farmer ( docs/ff_january_2017/42) and the latest developments in our studies of nutritional programming in salmon are reported elsewhere in the present issue. (The ARRAINA project produced booklets on Key Achievements, Nutrient Requirements and Biomarkers in Nutrition Institute of Aquaculture

08/05/2018 10:05:13

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You are what you eat…first! How nutritional programming can improve metabolic response By Xu Gong THE development and application of sustainable feeds formulated with low levels of the marine ingredients, fishmeal and fish oil, has raised concern about the declining levels of the beneficial omega-3 long-chain polyunsaturated fatty acids, EPA and DHA, in farmed fish. My PhD aims to determine the influence that the composition of diets at first feeding has on endogenous production and retention in order to maximise these processes, and the levels of these important nutrients in farmed Atlantic salmon. The first part of my studies is currently focusing on determining the potential of salmon for the endogenous production of EPA and DHA, and the impact that the dietary ratio of omega-3 to omega-6 fatty acids has on the biosynthetic process. This is part of an EU Aqaexcel2020 study, ENDOPUFA, led by Profs Douglas Tocher and Brett Glencross and carried out by the IoA’s Drs Monica Betancor and Matthew Sprague at the Institute of Marine Research, in Matre, Norway, with our collaborators Profs Rolf Erik Olsen and Ole Torrissen. The fish were fed for five months from first feeding with diets formulated without EPA and DHA, and with varying ratios of linolenic (18:3n-3) and linoleic (18:2n-6) acids. Analyses of samples from this trial is ongoing and will enable us to quantify EPA and DHA production in salmon in freshwater and how this is impacted by dietary fatty acid composition. For the rest of my PhD, I will be part of the University of Stirling team investigating the application in salmon of the ‘nutritional programming’ concept, which involves giving a nutritional stimulus at first feeding that will enable the fish to have an improved metabolic response when fed a similar diet later in life. An initial trial run as part of the recently completed EU FP7 project, ARRAINA, used a feed with very low levels of EPA and DHA as the stimulus/ challenge. The trial design involved initially feeding salmon larvae with either a stimulus diet (low EPA+DHA) or a control diet (high EPA+DHA) for a short period of time at first feeding, after which all fish were fed the control diet for several months

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Below: Xu Gong

before all fish were challenged with the low EPA+DHA diet. This study confirmed that nutritional programming can operate in Atlantic salmon in freshwater, and led to metabolic adaptations that enhanced the capability of the fish to thrive on sustainable feeds with very low marine ingredients. These adaptations led to improved growth and nutrient utilisation in the programmed fish, with retentions of EPA and DHA being particularly enhanced. A new project, NUTRIPROG, beginning later this year, is a BBSRC Industrial Partnership Award led by Profs Tocher and Glencross and Dr John Taylor with BioMar as the commercial partner. This will first investigate the duration of the stimulus period to determine the minimum time that the stimulus diet needs to be applied at first feeding, to ensure programming without affecting phenotype, such as fish size. A second trial will last 18 months from first feeding through smoltification and seawater transfer to around six months post-transfer. The primary objective will be to determine the long-term impacts of programming to ensure it operates in salmon in seawater when the greatest benefit, in terms of growth and nutrient utilisation and retention, will be achieved. A secondary objective of this trial is to determine the influence of nutritional programming and the timing of the application of challenge feeds on the key physiological processes of smoltification and seawater adaptation. The outputs of my PhD will help to establish and facilitate the application of the nutritional programming concept in commercial salmon farming operations, but they may also reveal that while the old adage, ‘you are what you eat’, is still true, the first meal may be the most important in life!

These adaptations led to improved growth and nutrient utilisation


08/05/2018 10:08:00

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Harvesting ‘fish oil’ from the land: the Camelina story

THE search for sustainable alternatives to fish oil as a source of the long-chain omega-3 fatty acids eicosapentaenoate (EPA) and docosahexaenoate (DHA) for feeds is one of the major issues in aquaculture today. As wild fish stocks diminish, while the global population increases, more pressure is placed on aquaculture to provide fish naturally rich in these omega-3 fatty acids, which have beneficial effects in the human diet. However, there are major sustainability and economic issues associated with depending on fish oil as the main source of omega-3 fatty acids used in aquafeeds, as its annual production is finite and limited. Replacing fish oil is challenging because EPA and DHA are not naturally found in terrestrially sourced ingredients. These fatty acids are, in fact, made predominantly by microalgae at the base of the marine food web. Although microalgae are now being produced using fermentation technology, production costs have, until now, been high and therefore it has not been economically feasible to use microalgae at high inclusion levels in fish feeds. Therefore, agricultural vegetable oils, such as rapeseed oil, are currently the main replacement for fish oil in the formulation of feeds, given their relatively low price and overall availability. Vegetable oils (and most animal by-product oils) are devoid of EPA and DHA, but rich in shorter chain, largely omega-6, fatty acids. This change in the composition of the feeds has impacted on the levels of EPA and DHA supplied to the fish, meaning that farmed fish such as salmon accumulate lower levels of these beneficial fatty acids compared to a decade ago. This translates into consumers having to eat double the portion size of fish compared to 2006 in order to attain the levels of EPA and DHA recommended by health advisory organisations. So while fish can be successfully grown on feeds containing high levels of vegetable oil, this changes their nutritional value, decreasing the content of the beneficial EPA and DHA in the fillet. The question, therefore, was whether it would be possible to design an oilseed crop that could produce 16

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Opposite page: Experimental tanks used for the sea bream trial at the University of Las Palmas de Gran Canaria. Bellow: Close-up of GMCamelina sativa or false flax. It is phenotypically identical to the wild-type crop, diverging only in the fatty acid content of their seeds. Courtesy of Rothamsted Research.

‘fish oil’ in its seeds. This approach was taken by Professor Johnathan Napier at Rothamsted Research in Harpenden, whose team demonstrated that it was possible to genetically engineer plant seed oils to accumulate EPA and DHA. This novel production platform and modified oil then formed the basis of multiple collaborative projects with Professor Douglas Tocher from the Institute of Aquaculture. Their long collaboration, mostly funded by the Biotechnology and Biological Science Research Council (BBSRC), was focused on tailoring a crop that could produce, entirely de novo, levels of EPA and DHA in seed oils ideal for aquaculture feeds. The plant of choice has been Camelina sativa, also known as gold-of-pleasure or false flax (Figure 2). Although it might not sound familiar, the plant has been cultivated in Europe since the Bronze Age for its nutritious seeds and oil. At present, it is grown as an oilseed crop, mainly in the US and Canada, where it has also been investigated for use as biofuel. Camelina seeds contain around

Institute of Aquaculture

08/05/2018 10:12:56

Designer diet

40% of oil, and the technology for harvesting the plant and oil extraction is essentially identical to that used for other oilseed crops, such as rapeseed. The oil derived from camelina is rich in short-chain omega-3 fatty acids and, therefore, by adding genes from microalgae, the genetically modified (GM) camelina becomes capable of producing and accumulating the long-chain omega-3, EPA and DHA, in its seeds. Thus, several types of modified camelina crops have been developed producing seeds with different oil profiles, containing EPA only or EPA and DHA, and over 25% of long-chain omega-3. Several camelina field trials have been performed in both the UK and North America, testing different GM varieties for their performance in the real world, with promising results. Over the last five years, I have been testing the oils from GM camelina crops in fish feeds. Several funders, including the BBSRC, the Research Council of Norway and the European Commission, have enabled us to perform, to date, six different trials, in Atlantic salmon, gilthead sea bream and European sea bass, to test this new de novo source of omega-3 as a substitute for fish oil. In 2013, (with a BBSRC Industrial Partnership Award with BioMar UK) tests were carried out with an EPA-only oil (20% EPA) and an EPA+DHA oil (6% EPA + 5% DHA) in feeds for Atlantic salmon post-smolts. The inclusion of both GM derived oils had the anticipated beneficial effect of increasing the levels of long-chain omega-3 in the salmon fillet while, at

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We have a viable and sustainable solution to the supply of long-chain omega-3 within reach


the same time, having no negative consequences for growth of the fish. These two oils were subsequently tested in feeds for sea bream in the facilities of the University of Las Palmas de Gran Canaria (thanks to the support of an EC Transnational Access Aquaexcel grant). This study showed the GM derived oils effectively promoted accumulation of both fatty acids in bream tissues without compromising fish performance (Figure 3). In a second phase of the research, a third generation of the GM camelina oil, containing both EPA and DHA that supplied total long-chain omega-3 at over 25%, higher than many fish oils, was tested. Two more trials in salmon were supported by a Norwegian Research Council grant to the Norwegian University of Science and Technology (Trondheim), University of Stirling and Rothamsted Research, along with BioMar as industrial partner. The successful performance achieved in the first


08/05/2018 10:12:06

Institute of Aquaculture

phase was with feeds with levels of fishmeal higher than commercially applied; the second phase then focused on feed formulations reflecting present Norwegian formulations. This meant reducing the fishmeal content of the feeds, as well as using a blend of rapeseed oil and fish oil in the reference (control) feed in order to reflect current commercial salmon feeds. As a result, the reference feed contained EPA + DHA at around 6% of total fatty acids, which corresponded with the level commonly applied in standard Norwegian feeds. Salmon given the feeds containing the GM derived oil accumulated almost double the levels of EPA and DHA in their body and fillet than fish fed the standard reference feed (reflecting current commercial formulations containing low levels of marine ingredients). Furthermore, this oil also supported good growth without any apparent negative impacts on fish health. This oil is now currently being tested in a new EC Aquaexcel funded trial in sea bass. While highly successful, none of the above trials in


The results of this trial will help establish just how efficient the GM camelina oil is as a substitute for dietary fish oil


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Above: Fig.1: The use of more sustainable feeds has dramatically reduced the EPA+DHA contents in Atlantic salmon with consumers requiring double the portion of fish to achieve recommended levels. The GM Camelina high in long-chain omega-3 could boost the EPA+DHA levels in salmon fillets.

salmon have been performed in harvest size fish, given the limited availability of the new designer oils. It is now necessary to evaluate whether all the positive outcomes observed in relatively small fish (post-smolts up to around 300g) can be extrapolated to large fish of greater than 4kg. This is the aim of a BBSRC Super Follow-on-Fund project that is live at the moment. This is a very challenging project that first requires the production of hectares of GM camelina crop to produce several tonnes of seeds. These have to be crushed to obtain sufficient oil to perform a long-term sea pen trial with Atlantic salmon, from smolt up to commercial harvest size. The first batch of seeds has been harvested, diets manufactured and the fish feeding trial will commence soon, lasting until summer 2019. The results of this trial will help establish just how efficient the GM camelina oil is as a substitute for dietary fish oil. We have a viable and sustainable solution to the supply of EPA and DHA for aquafeeds within reach. While the adoption and application of these oils in the UK and Europe will likely still face some hurdles, their expected use in other regions (the Americas, for example) will help to relieve the pressure on fish oil stocks, and could have a positive impact on omega-3 levels in farmed fish in the UK and the rest of Europe. For further information please contact

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08/05/2018 10:12:27

IFFO, the Marine Ingredients Organisation

Recipe for top research Working with the IoA uncovers scope of by-products in aquafeed IFFO, the Marine Ingredients Organisation, is an international trade body that represents and promotes the interests of the marine ingredients industry, particularly fishmeal and fish oil producers. With headquarters in London, and offices in Beijing and Lima, IFFO’s work spans the globe, covering production, markets, regulation and science behind these important animal feed and nutraceutical ingredients. Fishmeal and fish oil are extremely important products in aquafeeds in general, and the nutritional contribution they provide cannot be delivered by alternatives in a cost-effective manner at the volumes currently produced. IFFO is an evidence based organisation that relies on the provision of good quality science, and the organisation has a several decades long history of working with research providers, including the Institute of Aquaculture at the University of Stirling. In recent years, IFFO has benefited from the work that has been delivered by Dr Richard Newton within Prof Dave Little’s Society and Technology Interface team. Raw material supply for fishmeal and fish oil production is fundamental to the sustainability of the industry. This is split between whole fish, such as the small pelagic species (Peruvian anchovy, for example) and by-product on a 2:1 ratio, with an annual supply of approximately 20 million tonnes. In 2015, Newton was commissioned by IFFO to look at the availability of that raw material for fishmeal and fish oil production that was being utilised from seafood by-product, in order to calculate how much of the by-product was being used, and how much could theoretically be used if all that material is collected. His work concluded that there is significant scope for recovery of more by-product from both fisheries and aquaculture than is currently being achieved, with an estimated 11.7 million tonnes of material currently not being used. That material, once processed, could provide more essential ingredients to support the continued growth of aquaculture worldwide, including the ever important fish oil (and especially the long chain omega-3 fatty acids EPA and DHA). Some elements of Newton’s work were continued through IFFO’s support to three MSc in Sustainable Aquaculture students in 2016. Those students - Alban Caratis, Jean Peignon and Julien Stevens - all investigated different aspects of by-product recovery and utilisation in the Scottish fisheries and aquaculture industries. Stevens’ work on opportunities for added

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Above: Fishmeal in bowl. Below: Atlantic salmon by-products - The rise of aquaculture by-products - Stirling-IFFO study, February 2018

That material, once processed, could provide more essential ingredients to support the continued growth of aquaculture worldwide

value in Scottish farmed salmon by-product utilisation developed a categorisation hierarchy that will be used in some continuing project work with Newton in the future. IFFO supported Stevens in his writing up of the results of his MSc project thesis into a paper1 that was published early in 2018, and receiving much attention across the seafood media. Newton will now be looking at taking some of those results further forward within a development of the Fish In: Fish Out (FIFO) ratio, which has commonly been used to criticise the marine ingredients industry in the past, but which had failed to recognise the important nutritional contributions that the materials make. As well as Dr Newton’s work, and continuing the strong links between IFFO and the Institute, IFFO has recently commissioned Prof Brett Glencross to look at the quality parameters in the global fishmeal products, investigating the factors that supply nutritional, health and welfare benefits to a range of farmed aquatic and terrestrial species. This work is equally important to IFFO in establishing the true value of the contributions supplied by marine ingredients in aquafeed and animal feed, crucial information that feeds into bioeconomic models and the marine ingredients industry’s sustainability. IFFO looks forward to continuing strong links with the Institute, and with a developing base of technical projects over time, there may well be more project work to come in the future. 1 Stevens, J.R, Newton,R.W.,Tlusty, M.and Little, D.C. 2018. The rise of aquaculture by-products: Increasing food production, value, and sustainability through strategic utilisation Marine Policy, 90. 115-124


08/05/2018 10:15:06

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Deep sea world Investigating ocean omega-3 oil production in a changing climate By David W Pond, Daniel Mayor and Michael Leaver DEVELOPING an understanding of planktonic production in the Arctic, in the context of ice loss and warming, is the subject of the £2.5 million DIAPOD project. The NERC funded study, part of a wider £16 million UK investment into a Changing Arctic Ocean Programme, involves a number of national and international partners and is led by the IoA’s Prof David Pond. The research has a particular focus on zooplanktonic copepods, a critical link in transferring omega-3 rich oil and protein to support fisheries productivity. From May, Prof Pond will be leading a cruise to the Fram Strait (the passage between Greenland and Svalbard) on board the RRS James Clark Ross, collecting marine life from surface waters down to depths of 2km. The North Atlantic and Arctic oceans are experiencing rapid environmental change and modelling predictions suggest that warming and increased stratification of the water column will lead to profound changes in plankton communities. The UK and many other countries that border the Atlantic and Arctic oceans are heavily reliant on these marine environments for the commercial fisheries they sustain, which support human health and aquaculture by the provision of omega-3 rich oils. Zooplanktonic copepod species of the genus calanus are rice grain sized crustaceans, distant relatives of crabs and lobsters that occur throughout the Arctic Ocean, consuming enormous quantities of microscopic algae (phytoplankton).


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These tiny animals represent the primary food source for many Arctic fish, sea birds and whales. During early spring, calanus gorge on extensive seasonal blooms of diatoms, omega-3 rich phytoplankton that proliferate both beneath the sea ice and in the open ocean. This allows calanus to rapidly obtain sufficient fat to survive during the many months of food scarcity during the Arctic winter. Calanus seasonally migrate into deeper waters, to save energy and reduce their losses to predation, in an over-wintering process called diapause that is fuelled entirely by carbon rich lipids. This vertical ‘lipid pump’ transfers vast quantities of carbon into the ocean’s interior and ultimately represents the draw-down of atmospheric carbon dioxide (CO2), an important process within the global carbon cycle. Continued global warming throughout the 21st century is expected to exert a strong influence on the timing, magnitude and spatial distribution of diatom productivity in the Arctic Ocean. Little is known about how calanus will respond to these changes, making it difficult to understand how the wider Arctic ecosystem and its biogeochemistry will be affected by climate change. Calanus and other zooplankton productivity is directly linked to fisheries productivity, including those fisheries which provide meals and oils for aquaculture. To sustainably manage these fish populations in the face of environmental change, fisheries scientists based in the UK and overseas need to be able to accurately model the lifecycles of the key species of calanoid copepods to predict how environmental change will impact on copepod population dynamics and distributions. This knowledge will be essential for understanding future consequences for fisheries productivity and sustainable exploitation of natural omega-3 resources. Two studentships are linked to DIAPOD: • Euan McRae, of the University of Strathclyde, will explore trait based modelling of large crustacean zooplankton of the Arctic and Antarctic. The research aims to adapt and expand DIAPOD to include krill and Antarctic copepod Institute of Aquaculture

08/05/2018 10:18:20

Deep sea world

species, thereby extending this work to the southern oceans, another major source of fishmeal and oil. • Holly Jenkins, based at the National Oceanography Centre in Southampton, will look at the ecological stoichiometry of Arctic zooplankton. The project focuses on Arctic zooplankton, more specifically copepods, and their physiological budgets. The research will investigate ecological stoichiometry, and relate the omega-3 composition of the copepods to the composition of their food. Professor David Pond has recently joined the Institute of Aquaculture and brings expertise related to the ocean processes and ecosystem functions that give rise to the fish stocks and other marine resources that provide meals and oils for aquaculture feeds. Such research will be invaluable in guiding the future sustainability of aquaculture activities worldwide. David Pond and Michael Leaver, IoA; Daniel Mayor, National Oceanography Centre, Southampton For further details, please contact David.Pond@stir. or For full details of DIAPOD see (https://www.changing-arctic-ocean. Above: RRS James Clarke Ross, the research platform for the DIAPOD and NERC Changing Arctic Ocean programme. Inset: Calanus finmarchicus. Far left: A typical ‘pink’ plankton net haul form Arctic waters indicating the high biomass of calanoids and krill in northern latitudes Bottom left: Calanus hyperboreus.

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Such research will be invaluable in guiding the future sustainability of aquaculture


08/05/2018 10:18:36

Institute of Aquaculture

Metamorphosis Innovations in insect meals for the carnivorous fish feed sector A £900,000 project to develop insect processing solutions for aquafeed was launched at the IoA in February. The two-year Metamorphosis initiative, funded by Innovate UK and headed by Dr Oscar Monroig and Dr Simon Mackenzie, is investigating the use of insect meal products from the black soldier fly (Hermetia illucens) in feeds for Atlantic salmon. Feeds for fish farming have been traditionally formulated with remarkable levels of marine ingredients, particularly fishmeal and fish oil, primarily derived from wild capture fisheries of low grade species such as the Peruvian anchovy. Production of fishmeal and fish oil is finite and, with the expansion and diversification of aquaculture often involving carnivorous fish species with high commercial value, alternative raw materials to Below: Feeding trial formulate diets have been extensively investigated. facilities at Buckieburn Plant and land animal derived ingredients have (from the Photo Bank). been commonly used to replace fishmeal and fish Opposite: Black soldier fly oil in aquafeeds for carnivorous fish such as salmon, larvae (Photo: Entomics). but certain issues associated to their use result in further alternatives being still required. Insect meals are a very promising option. The use of insects for aquaculture feed only be-

came legal in the EU in July 2017, and the market is expected to grow rapidly. Several research projects have confirmed that insect meals have many beneficial properties, but also have some hurdles to overcome. The Metamorphosis project will explore strategies to improve the effectiveness of these insect derived feed products. It aims to develop a suite of novel insect bioprocessing approaches, providing opportunities for generating protein enriched and chitin deprived insect derived meals, particularly relevant for the carnivorous fish feed sector. The project will also benefit from the involvement of global fish feed manufacturer BioMar, which will prepare the experimental diets at BioMar Technology Centre in Brande, Denmark. Dr Monroig said: ‘Insect meals are being increasingly recognised as perfectly suitable ingredients for farmed animals, including fish. It is worth noting that salmon can feed on insects while they are growing in the river before migrating to the sea, and therefore are naturally adapted to these food items. ‘Thus, the insect meal products developed during the duration of the project will be used not as a mere fishmeal replacement alternative, but rather as a feed ingredient for functional feeds aiming to enhance health of fish.’ The project will further explore how insects have to be processed to enhance feed utilisation and health status of salmon. Metamorphosis is led by Entomics Biosystems (, a company founded by four Cambridge graduates with backgrounds including biochemistry, engineering and finance. Entomics develops insect meal products that have added functional benefits, in addition to providing key nutrients.

This is another step towards gaining wider market understanding and acceptance


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08/05/2018 10:19:44


The company, supported by Reading University, is seeking to work with leading and emerging producers of black soldier fly larvae in producing new insect products for a series of animal feed sectors. The larvae of the black soldier fly have a great appetite and they are able to efficiently metabolise low-value food waste into important nutrients such as proteins and fats. Humans produce more than 1.3 billion tonnes of food waste per year, which is around a third of all the food we produce. Taking advantage of this waste to grow insects could help cut waste and greenhouse gas emissions linked to the production of this food. Matt McLaren, CEO of Entomics, said: ‘These insects can grow on a variety of organic waste sources, so there is huge opportunity to create a sustainable new ingredient for the global animal feed sector. ‘We feel the Metamorphosis project is critical to unlocking the value of insect derived feeds for the salmonid aquaculture industry specifically.’ The IoA will be responsible for assessing the performance of the insect meal products in fish, and trials with freshwater and seawater salmon will be

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run during the project at the university’s facilities in Buckieburn and Machrihanish. To aid with this work, Stirling has appointed Dr Clara Mackenzie as a post-doctoral research assistant on the project. Dr Mackenzie is a recent PhD graduate of Heriot-Watt University and brings her expertise in the cellular and molecular stress responses of marine species to the project. She will support the assessment of health impacts and feed performance, carrying out cell culture and gene expression aspects of the programme. Stirling also aims to build project collaborations with other emerging research programmes, to bring added value to the project, develop project outputs, and extend research directions into other innovative areas of investigation in the field. Overall, this project reflects a circular economy approach to solving some of the key challenges related to sustainable aquaculture feeds of the future, and is another step forward towards insect derived feeds gaining wider market understanding and acceptance. For further information, please contact Oscar Monroig ( 23

08/05/2018 10:20:03

Community benefit – Scottish Sea Farms

Getting to the heart of the matter How supporting local projects has helped build trust By Jim Gallagher OPEN, honest, ongoing dialogue with the communities in which we work and live has never been more important – for Scottish Sea Farms or for the sector. Engaging with younger generations via school visits and farm tours. Hosting open days for the wider public. Consulting closely with local residents and groups on planning applications and developments. These are all activities that the sector is involved in on a regular basis to help build and maintain relations with the communities in which we farm. Scottish Sea Farms, however, operates one additional initiative alongside these; an initiative without any agenda other than to give something back, but one that has had a huge bearing on the way our company and farms are perceived locally. Heart of the Community Heart of the Community was introduced back in 2011 to support local causes, groups and projects


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across our three business regions of mainland Scotland, Orkney and Shetland with grants of anything between a few hundred pounds and £10,000. In the seven years since, that’s added up to 302 supported projects and an investment of £920,581 – and we’re on course to top the £1 million mark later this year. The real value, though, lies in the nature of the projects supported. Engagement at every level Each and every project that we support is nominated by a local group or organisation and approved by our regional team - people who not only work in the community but also live there, raise their young families there and retire there. As such, they know first-hand the issues that remote and rural communities can face, and where Heart of the Community support would help the most. Together, we are: • Creating affordable, family oriented activities – from funding new and improved play areas, to supporting mother and toddler groups where mums can share experiences and young tots can interact; • Encouraging younger generations to remain in their communities – ensuring that young athletes such as the newly crowned league champions Orkney Football Club have the same opportunities to compete in tournaments as those living in more central locations; • Developing resilience from an early age – co-funding youth clubs and junior sports teams where youngsters can have fun while learning vital life skills such as teamwork and leadership; • Tackling dependency and depression – helping those dealing with alcohol or drugs dependency, suffering from depression or having suicidal thoughts to get much needed support; • Combating isolation – everything from co-funding community transport or buying iPads for care home residents so that they can FaceTime friends and family, to supporting one-to-one art therapy sessions for dementia sufferers; • Providing lifeline services – helping reduce the risk of cardiac arrest through the provision of vital

Clockwise from top right: Orkney FC; mother and toddler group; the M&S Rural Community Award; the Ulva Ferry Community Bus; SSF iPads; dementia art therapy.

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08/05/2018 10:21:43

Getting to the heart of the matter

We’ve gone from ‘one of them’ to ‘one of us’

screening services and ensuring that those at risk of domestic abuse get the support they need. It’s the everyday yet essential nature of projects such as these that saw Heart of the Community win the Rural Community Award at the M&S ‘Farming for the Future’ Awards 2016. Raising awareness At a local level, Heart of the Community has helped open up a genuine dialogue, establish closer ties and, in turn, earn us the trust of our communities. We’ve gone from ‘one of them’ to ‘one of us’, not because we’ve invested on a huge scale in technology, salaries, career development or health and safety – all of which we have – but because we’ve simultaneously invested in the areas that mean most to the communities themselves, adding value beyond the business and into their homes and daily lives. Jim Gallagher is managing director of Scottish Sea Farms

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08/05/2018 10:22:03

Institute of Aquaculture

Best of two ‘mums’ Triploid salmon research aims to get the recipe right IT has been debated as to whether triploid salmon could or should be considered within the UK salmon industry. While commercial scale deployment is now well underway in Norway, in part stemming from requirements for new R&D and green licences, the Scottish approach has been somewhat slower and more conservative. The production of triploid fish is not a new concept and has a long history of use in both aquaculture and sport fisheries management. They [triploids] also occur spontaneously in nature, a facet that can be harnessed and artificially induced. Producing a triploid egg is relatively easy in salmo-


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nids, utilising specialist equipment to apply a hydrostatic pressure ‘shock’ (equivalent to holding eggs at a depth of 6,500m for few seconds) at a critical temperature development point, not long after fertilisation. Correct timing is essential in order to achieve a desired 100% triploid rate. However, from the moment that egg is fertilised, if not before, there are many steps in growing them that need to be right, in order to get the best from a triploid, in part due to their genetic and cellular make-up. Triploidy itself refers to the condition of having three complete sets of chromosomes in the genome and occurs through duplication of the maternal genome, compared to the diploid state, where one set is inherited from each parent. The most appealing feature that triploidy offers is that it renders the animal sterile. Sterility offers a unique solution to address simultaneously three key salmon industrial challenges: prevention of reproductively competent escapees; avoidance of

Institute of Aquaculture

08/05/2018 10:23:58

Best of two ‘mums’

Above: Evidence of improved mineralisation (more intense pink staining) of triploid spinal column at 3 weeks old when fed increasing dietary phosphorous levels.. Opposite page: Evolution of improved egg survival of triploids (red) relative to diploids (blue) at both experimental (expt.) and commercial (comm.) scale production from 2007 to 2017 following refinement of induction process and incubation protocols.

flesh quality deterioration associated with pre-harvest maturation; and potential for enhanced productivity through better growth. However, while all sounding positive, triploids have historically been characterised by lower survival, increased deformity, and reduced performance under sub-optimal rearing conditions. While the most striking feature of triploids is the increased genome size, there is also a concurrent increase in cell size and reduction in cell number. The potential impacts of these features on the fish metabolism and physiology have, until recently, been poorly characterised. For the last decade the IoA has coordinated a series of industry, nationally and internationally funded research projects to examine triploid physiology in order to solve production bottlenecks and improve performance traits. The current research programme, SALMOTRIP+, now in its third phase and supported by a joint BBSRC and INNOVATE UK award, is a £2.2 million project coordinated by Dr John Taylor and Prof Herve Migaud, in collaboration with key industrial partners Marine

Sterility offers a unique solution to address three key industrial challenges

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Harvest Scotland, BioMar and Pharmaq (part of Zoetis). The project is centred around five main work packages: genetics and breeding; nutritional requirements; health management; environmental impacts; and, potentially most important, commercial scale benchmarking. Research activities have been supported by a team of post-docs - Drs Elsbeth McStay, Luisa Vera, and Stefano Carboni - and PhD students Dr Marie Smedley, Dr Lynn Chalmers and Michael Clarkson, not to forget a host of BSc and MSc research dissertation projects over the years. Does extra maternal contribution matter? One attribute under investigation is whether more attention should be paid to the influence of the extra set of genetic material provided by the mother. Evidence certainly suggests an additive genetic effect for growth, and the question remains what effect this is having on other traits. There is a clear need to understand inheritance patterns within triploids to support future selection. Similarly, we actually know very little of the mechanisms of gene regulation and cell-mediated pathways in triploids as a whole, and these will be key to understanding how we can harness the beneficial traits. Also under investigation is the contribution of the egg quality aspect of the mother. Triploid eggs were associated with higher losses, attributed to additional ‘physical’ handling during the induction process. Following tagged fish from evidently ‘poorer quality’ egg batches has identified that the survivors continue to be 27

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the poor doers all the way to harvest. Being able to determine egg quality, and avoid the poor doers, may help in part reduce the greater variability observed within a triploid population, which increases losses when grading out runts, and makes for more challenging stock management and harvest weight consistency. But what makes a poor quality egg when inducing triploidy? We are currently characterising biomarkers of egg composition and shell integrity associated to egg ageing post ovulation, hypothesising that aged eggs cannot handle the added ‘stress’ of the pressure shock, which may contribute to increases in egg mortality and population variation. Collectively, our evidence suggests that if we do not start with optimal egg quality and subsequent first feeders, then we may be facing an uphill battle as we try to manage the on-growing traits in triploids. Over the last 10 years, research performed at the IoA has led to a better understanding of these traits in triploids and refined husbandry, and it is evident we have seen marked improvements in triploid viability in both experimental and, more importantly, commercial scale production batches (Pic 1). Nutritionally dense diets: unlocking growth potential and preventing deformity Triploids have inherently faster growth, provided that they are given a feed that covers their nutrition28

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The spread of viral prevalence within triploids is slower, which may suggest greater resistance

Above: Evidence of loss of weight advantage in triploids (red) relative to diploids (blue) in late summer during seawater grow out, related to the subsequent reduction in feed intake during warmer water periods.

al needs. Higher prevalence of deformity has also been associated with triploidy. However, advances in screening methodologies (X-ray, for example) have revealed that in most farmed fish, there is a degree of skeletal deformity, but the question is at what level does it compromise the animals welfare and/or impact on harvest quality. Thanks to recent research on triploid nutritional and environmental requirements and availability of new triploid specific aquafeeds, we are now seeing triploids with comparable deformity prevalence rates to diploids. In virtually all trials conducted, freshwater growth to smolt in triploids can be in the region of 15-25% faster than their diploid siblings; however, sustaining this enhanced growth potential during the seawater phase has been more challenging. Research collaboration between the IoA and BioMar led to a bespoke range of triploid specific diets. Triploids require more protein, specific amino acids, Institute of Aquaculture

08/05/2018 10:24:38

Best of two ‘mums’

vitamins and minerals. For instance, increased supplementation of the essential amino acid histidine is key during risk periods of rapid growth (early summer) and smolt entry to sea, in order to prevent cataract formation. Similarly, supplementing dietary phosphorus (P) during freshwater feeding is essential for the correct mineralisation of the skeleton (Pic 2). Phosphorous is used in virtually all cell processes, including energy metabolism and DNA synthesis, so just by virtue of being alive there is a requirement, and with a genetic make-up encoding more growth, then dietary P deficiency easily occurs when triploids are fed a diploid formulation, as was done in the past. However, boosting the diet with certain nutrients can not only be financially costly, but may also increase environmental discharge. In particular, the higher requirements of triploids in P throughout freshwater is a concern as it could limit biomass production consents. In light of this aspect, we have been refining formulations and determining windows of requirement for P. We are now able to restrict the period of feeding high P diets to the first few weeks in freshwater, without compromising skeletal integrity. Furthermore, we have had exceptional results using probiotics (Bactocell®) as a means to improve nutrient assimilation, allowing further reduction of nutrient inclusion levels. But the diets, and their beneficial effects, can only be seen if triploids have been produced optimally from the start, with fry in optimum conditions.

While, in general, mortality post-treatments has been low and comparable between ploidy, we clearly see that in warmer sea temperatures there is increased risks in triploids. This does, however, appear to be related to crowding stress in summer at specific sites, rather than the treatment itself. As such there is a clear need to define operational protocols for handling, and examine site specific environmental characteristics for deployment.

Deployment in favourable environments It is well known that triploids cope less well during periods of warmer temperatures and lowered oxygen, and this may be the single biggest factor contributing to reduced seawater growth potential, rather than increased disease susceptibility or deformity. In particular, there is a noticeable drop in feed intake of triploids when sea temperature exceeds 14-15°C (Pic 3) which is further accentuated when exposed to additional challenges. On the flip side, triploid feed intake is generally greater in cooler temperatures, a necessity to support their higher growth rate, and this Slowing embryonic development to build a better body may explain documented cases of triploids performing Experimental and commercial trials have now shown that lower jaw deformity (LJD) can be prevented in triploids. Original research focused on a dietary fix during well in Northern Norway. Interestingly within the project, producing triploids marine grow-out, as LJD only manifested during this phase. While helping, diets did in more constant temperature RAS sites has produced not alleviate the problem entirely. bigger smolts, with improved skeletal health at harBoth the IoA and colleagues in Norway have shown that LJD is of embryonic origin. By simply incubating triploid eggs at a lower temperature than conventional vest, than those from more environmentally fluctuatdiploid regimes, in effect slowing the rate of embryo development, prevalence rates ing flow-through sites. Producing triploids in a more stable environment can now be less than 1%. may indeed be key to unlocking their potential. This Preventing LJD has been one of the biggest steps forward in improving triploid apparent better performance in constant temperature stock robustness, as affected fish may have reduced respiratory capacity. environments is an interesting thought for the future Similarly, spinal development in triploids is equally temperature sensitive during embryogenesis, and again spinal formation can be significantly improved by lower- triploids may be worth exploring for use in land based ing initial egg incubation temperatures (see article by PhD student Michael Clarkson RAS systems, where maturation rates, in particular, have been very high. within this issue). There may even be scope to consider their deployThese temperature induced traits appear to originate from collagen disruption ment in more offshore sites, where stronger currents when forming skeletal structures during embryogenesis, with rapid seawater may provide more favourable environmental condigrowth ultimately accentuating any defects in the architecture. tions. In addition, their sterility, may be a safeguard Results of the studies certainly support the concept of ‘slowing embryogenesis against potential system failure and escapes in these to build a better body’ when referring to triploid development. However, lowering high energy environments. incubating temperatures does increase incubation duration and affect production planning logistics. Getting the best from your triploids This can be offset by producing triploid eggs from earlier spawning broodstock, Research to date has provided clear evidence that and carefully planning intake and orders. That said, lowering egg incubation temthere is a need to align all the pieces of the puzzle perature also appear to increase muscle fibre recruitment, which could result in a to achieve the desired and most effective results; in fish that grows faster once feeding. effect, we need to get the ‘triploid recipe’ right. What is clearly evident is that triploid eggs must be Defining robustness: disease challenge and treatment tolerance incubated from fertilisation at lower temperatures than Good results have been obtained from both field and lab challenges to paraconventional diploids; their dietary requirements are sites (amoebic gill disease, AGD, caused by Neoparamoeba perurans and sea lice, higher at key developmental phases; and that they Lepeophtheirus salmonis), bacteria (A. salmonicida), and viral infections (salmonid must be deployed within the right environmental conalphavirus, SAV, and infectious pancreatic necrosis, IPN), with no differences in ditions. Couple this with potential to gain more from mortality between ploidy. Of interest, as observed by other colleagues in the field, is that the spread of viral selective breeding, then we could be a considerable prevalence within triploids is slower, which may suggest greater resistance, but this way to getting the best from our triploid stocks. So where does this leave us in Scotland? Given the remains to be conclusively proven. encouraging, but variable, results to date, there apHowever, we do see, as observed in Norway, that triploids are more predisposed pears to be a need to more closely scrutinise the envito winter sores (moritella). This skin associated disease again could be related to ronmental characteristics of the sites in which triploids differences in cellular make-up (less, but bigger, cells in triploids) and functional are deployed within Scottish waters, and consider the differences in number and size of wound healing cell types. timing of smolt input with respect to environmental Commercial field trials, albeit nervy at times, have also provided good documenconditions likely to be experienced. tation of tolerance to handling and treatment procedures, ranging from various bath treatments, to hydrolicer and thermolicer. For further information, please contact project coSimilarly, triploid response to commercial vaccines licensed in the UK is no different to diploids, and they handle commercial scale automated vaccination processes ordinators, Dr John Taylor ( or Prof Herve Migaud ( well.

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08/05/2018 10:24:55

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Nipping the gonad in the bud Alternative means of producing sterile fish by gene editing THE control of puberty in farmed fish is critical for the aquaculture industry because it can have adverse impacts on the health, welfare and productivity of farmed stocks. Furthermore, if farmed fish escape, there is a potential impact on the genetics of wild stocks through interbreeding. The Breeding and Stock Improvement research group has a long history of developing and implementing methods to mitigate the impact of maturation during commercial culture. Research over the past 20 years has validated a wide range of methodologies tailored to species and production systems requirements. These have included, photoperiod manipulation in species such as Atlantic cod and Atlantic salmon, monosex production in tilapia and Atlantic halibut, as well as triploidy in salmon, along with rainbow and brown trout. Building on this solid base of expertise, current research effort is being directed towards the development of the next generation of sterilisation methods that could be implemented across the industry in future years. PhD student Yehwa Jin initiated a programme of work focusing on the use of new gene editing technologies to knock out genes involved in the maintenance of germline cells in fish which, if implemented carefully, should result in sterile fish. Primordial germ cells (PGCs) are the origin of germ cell lineage, which ultimately will give rise to eggs and sperm within gonads in adult fish. Jin’s research aims to disrupt the development of these PGCs through gene editing to induce sterility in the adult Nile tilapia. In this research, tilapia was chosen for commercial as well as scientific reasons. Nile tilapia is one of the main finfish species farmed worldwide, with four million tonnes produced annually. In addition, productivity of the sector is reduced due to losses associated with maturation in culture, and while the industry addresses this challenge 30

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through the farming of single sex (all male) stocks, there is a clear demand for the validation of alternative effective sterilisation methods. As an experimental model, Nile tilapia has a number of key attributes, including a short generation time (only six months to reach adulthood). And thanks to the Breeding and Stock improvement group and its many international collaborators, there is extensive knowledge available on the species’ sex determination and differentiation mechanisms, as well as many tools - not least the full genome sequence, which was derived from stock produced at the Institute of Aquaculture. This PhD project first aimed to identify genes involved in PGC maintenance and survival which would subsequently result in the development of the testis. It is these genes which would then be targeted for gene knockout to then explore the viability of gene editing to induce sterility. Many candidates were screened to define their role during early embryonic development and, based upon results, one gene called piwil2 was selected as the best target. The next phase of the project aimed to investigate the function of piwil2 gene by using the CRISPR/ Cas9 methodology. This gene editing method has proven to be a very powerful biotechnology tool, and it has recently moved into the public domain, with multiple companies registering their intent to

Any large scale implementation would require the appropriate regulatory framework to be in place

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08/05/2018 10:40:53

Nipping the gonad in the bud

use it in the personal medicine field in 2018. In the context of the current research, this gene editing technique required the injection of eggs at the very start of their development, which will then result in the genes being inoperative as the embryos develop. A microinjection system was set up and validated to be harmless to Nile tilapia embryos and showed a capacity to inject more than 300 eggs per batch on a given day, which was ideal to conduct further research. The gene editing construct injected into the embryos consists of two essential molecules: a molecular scissor called Cas9 that cuts the DNA and a short RNA molecule called guide RNA which has sequence that matches that of the target genes sequence on the genomic DNA to guide the cut site of Cas9. Pools of embryos injected with this mix targeting piwil2 were incubated and larvae sampled following hatching to screen for individuals in which piwil2 gene had been edited. The method proved highly effective once optimised, with more than 90% of individuals being edited at the target gene. Each edited larva sample was also analysed by histology to confirm the presence or lack of PGCs, with more than 50% of the edited embryos having a physiological effect with either an apparent lack of PGCs (29%) or atrophy and/or locally restricted

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Above: Yehwa Jin

PGCs (25%). The remaining individuals (46%), while having an edited genotype, still possessed normal PGCs as was observed in control larvae. Overall, these results suggest piwil2 plays an important role in the survival of PGCs during early larvae development in Nile tilapia, and gene editing may be used to target the gene and sterilise individuals. However, more validation and refinement will be needed to increase the reliability of the technique. This work is the first demonstration of gene editing targeting the gene piwil2 using the CRISPR/Cas9 system, resulting in putative sterile fish in a commercially important farmed species. But this is still very early days in the development of this new technique and further studies are required to confirm the long-term sterility in fish with piwil2 knockout and overcome technical limitations associated with the delivery method and up-scaling. In addition, while this work has potential commercial applications, research is clearly fundamental at this stage. Any large scale implementation would require the appropriate regulatory framework to be in place. For further information, please contact Yehwa Jin (, Prof Herve Migaud (hm7@ or Dr Andrew Davie ( 31

08/05/2018 10:41:09

Institute of Aquaculture

Heat is off How low should you go with incubation temperatures for triploid salmon? THE demand for salmon is growing and in order for the industry to keep pace, we must adapt accordingly. Triploid Atlantic salmon have the potential to play an important role in the developing aquaculture industry. The fish are rendered sterile which can combat escapees from breeding with wild populations and also enhance growth potential. However, triploid salmon have previously been associated with a higher prevalence of bone malformations. Egg incubation temperature appears to be of particular importance, as triploids are thought to be more sensitive to temperature than diploids, and embryogenesis is a critical developmental onset. This has been studied as part of Michael Clarkson’s PhD , sponsored by Marine Harvest Scotland, BioMar and the IoA, under the supervision of Dr John Taylor and Prof Herve Migaud. The present project investigated the development of diploid and triploid salmon reared under different incubation temperatures (6, 8, or 10°C) during either a short (pre-hatch) or long (up to first feeding) window. Reducing egg incubation temperatures slows down development, which may be problematic for a well established commercial production cycle. The aim of the trial is to refine husbandry regimes during early egg incubation in salmon to promote optimal development and performance later on, and produce more robust stocks, while keeping in mind the production cycle duration. Such regimes are based on a deeper understanding of the underlying effects of temperature on key physiological functions in salmon, including the regulation of selected genes involved in bone and muscle development. Top: Salmon eyed eggs. Temperature is a very important factor during embryAbove: Michael Clarkson ogenesis in all animals. Humans and other mammals have the ability to regulate their internal temperature, whereas fish are directly influenced by the temperature of their surrounding environment, the definition of an ectothermic animal. This has been utilised to increase production of farmed salmon by speeding up development using elevated temperatures. Decades of research and industry experience has found 8 °C to be the upper threshold for optimal egg incubation temperature for a normal diploid population. Research into the use of triploid salmon in aquaculture has suggested that these individuals have very different nutritional and environmental requirements compared to their diploid siblings. Triploid specific diets have been developed and husbandry protocols have been adapted which have certainly reduced the negative attributes historically associated with triploid salmon. However, current research is demonstrating that increased prevalence of bone malformations in triploid


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salmon can be pre-determined prior to first feeding in alevins, and then manifests itself later during grow-out. Thus, it is likely that triploids have a lower thermal tolerance than their diploid siblings and only recently has this been considered during the embryogenesis stages. Overall, this study showed that incubating eggs at 6°C had positive effects on the development of both diploid and triploid Atlantic salmon. This simple husbandry refinement allowed the fish to utilise their yolk sac more efficiently and grow better, and it also result in a lower occurrence of spinal health problems in later life stages. However, it would extend the duration of a conventional production cycle. For example, incubating under a conventional protocol at 8 °C from fertilisation until first feeding takes roughly 16 weeks. If this temperature was lowered to 6 °C, that would be extended to 21 weeks. If we can incubate at 6 °C for only a short window, prior to hatching, this can both allow for the improved robustness of the fish with only minimal impact on the duration of egg incubation (18 weeks). These results are very encouraging for triploid Atlantic salmon aquaculture. They contribute to a better understanding of how climate change and the seasonal warming of water bodies would impact on fish development and robustness in wild populations. For further details, contact Michael Clarkson (mc63@, Dr John Taylor ( or Prof. Herve Migaud (

These results help understand how climate change would impact on fish development and robustness in wild populations

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08/05/2018 10:43:29

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Transfer technology A new approach to assessing smoltification in salmon

ATLANTIC salmon is currently the highest valued farmed finfish species globally. It accounts for 16.5% of the total fish produced in 2015, with more than 2.3 million tonnes produced (FAO 2015). Although in high demand, the production of Atlantic salmon is hampered by difficulties in husbandry management. One of the most prominent problems is identifying the correct time to transfer fish from freshwater to seawater. The Atlantic salmon is a migratory species that spends the first year of its life in freshwater. Once they reach a specific weight and body size they

Above: Michael McGowan

The ability to test on site and provide advice on the day will help farmers act quickly

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begin to undergo a physical transformation termed smoltification, where they adapt their body to life in seawater. Wild salmon can move downstream towards the sea as their bodies adapt, and eventually move out into the open ocean. This is not possible in the aquaculture industry as fish are kept within freshwater tanks throughout their development, before being transferred to seawater pens. This is a crucial period in their lifecycle as transferring too early can cause non-adapted fish to be more vulnerable to disease and mortality. Fish transferred too late can also suffer long-term health problems due to de-smoltification (regression to freshwater form). It is essential that all fish are transferred at the correct time to limit disease and mortality. Currently, enzymatic activity assays are the only diagnostic tool available to identify smoltification. However, this tool has varying results and does not always produce a clear picture of when smoltification has occurred. It is also restricted to in lab testing due to the toxic chemicals it employs. The research aimed to create a new diagnostic tool, applying quantitative real time polymerase chain reaction (qRT-PCR) technology for in lab and mobile diagnostic platforms, to compare with current industry standard enzyme assays over three years and for onsite testing at active hatcheries. Over the study period it was found that the PCR assay was as effective as the enzymatic assay, suggesting the PCR assay, due to its cleaner, easier and faster approach, is a candidate to become the standard approach for assessing smoltification. On site tests were successfully conducted at four sites, giving advice on the day as to whether the fish were ready to be transferred or not. As timing is crucial, any reduction in the time taken to decide on transferring is a major advantage. Looking to the future, the assays’ ability to add more biological markers would increase the effectiveness of the test and give farmers a clearer picture as to when smoltification has occurred. The ability to test on site and provide advice on the day will help farmers act quickly and ensure the optimal seawater performance of fish. This work was conducted by PhD student Michael McGowan in partnership with his supervisors, Manfred Weidmann and Simon MacKenzie, at the Institute of Aquaculture, and industry partners Europharma Scotland and PrimerDesign. Funding was provided by the Scottish Aquaculture Innovation Centre (SAIC) and Innovate UK. 33

08/05/2018 10:46:58

Community benefit – Marine Harvest

Perfect fit Marine Harvest’s 30-year sponsorship of shinty has helped rural culture thrive SHINTY has been described as a cross between Aussie Rules and Gaelic football, or hockey without the rules, a game invented to keep Highlanders warm in the winter. Deeply ingrained in Scottish rural culture, shinty might not command the mass following of football or rugby, but it is huge in Highland communities. In fact, in recent years Scotland’s most iconic indigenous team sport has witnessed a significant expansion, with membership growing 20 per cent since 2014. The Camanachd Association, the game’s governing body, said this has been achieved with the support of Scotland’s largest salmon farmer, Marine Harvest. When the Fort William based company decided to give something back to the areas where it farms, sponsoring shinty seemed a perfect fit. That was thirty years ago, and today Marine Harvest is closely associated with the shinty premiership, all the national leagues, and its international competition. It is also behind the expansion in both the women’s game and the youth leagues, ensuring the future health of the sport. In October last year, Marine Harvest agreed a new three-year, six-figure sponsorship of shinty, the largest ever single sponsorship investment in the Highland sport. Jim Barr, the then president of the Camanachd Association, said: ‘Shinty is an important part of Scotland’s sporting and cultural


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Above: Shinty/Hurling International at Bught Park, Inverness. Below: Scottish captain Finlay MacRae with the Marine Harvest quaich. Opposite page: (From left) Camanachd Association then president Jim Barr, president-elect Keith Loades, Steve Bracken, and Derek Keir sign the new deal in October 2017.

heritage and remains a key part of community life in many areas across the country. ‘Marine Harvest have been exceptional partners and have always made it clear their contribution is intended to give something back to the communities in which they operate. Consequently, they have been very flexible and always supportive of what is best for shinty.’ Marine Harvest Scotland managing director Ben Hadfield said: ‘Having supported shinty for 30 years we are very pleased to announce our continuing support for the game for another three years at all levels. ‘It has been very rewarding to see how the game has developed and grown, particularly with women’s shinty and the work and commitment that we’re seeing invested in youth shinty. ‘And, of course, we are delighted to continue providing the annual Marine Harvest National Shinty Awards which recognise the hard work and dedication of players, coaches and others in the sport. As we have said many times before, we are proud to be able to play our part in supporting the game.’ According to the Camanachd Association’s CEO, Derek Keir, the connection between shinty and Marine Harvest - which farms in the Western Isles, Skye, Argyll, Wester Ross and Lochaber - lies in a shared geography. ‘If you look at where a lot of their locations are, and the people who work for them, a lot are involved in our shinty clubs – as referees and as players. ‘We’re absolutely committed to supporting the local community in some of the rural parts of Scotland, to drive shinty forward and create more competitive opportunities for people to enjoy sport. ‘The Marine Harvest support helps us provide those competitive opportunities in rural parts of Scotland on a regular basis.’ The association held a consultation with its member clubs last year, said Keir, and it emerged that one of the biggest values in shinty is community. ‘We’ve got a number of players who go off to univerInstitute of Aquaculture

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Perfect fit

sity but they come back to represent their shinty club at the weekends. That stands shinty in good stead, that they are committed to representing their local community. ‘In the terms of the support and goodwill that shinty has, I think it stems from that sense of representing your local club. People know each other and value the fact that they can go to a cup final and people are representing their local communities.’ Keir said that between 2014 and the end of last year, the number of registered members has grown from 2,050 to 3,354. While the Camanachd Association receives about a third of its funding from the Scottish government and Sport Scotland to help cover the cost of its eight staff, the Marine Harvest sponsorship specifically helps with the Marine Harvest premiership and all the national leagues, providing trophies, medals, and prize money. The company supports the youth side as well, the under 17s and under 14s – another fast expanding group. At the end of 2017, there were 1,157 young male players compared to 1,437 adult males, and 337 young females alongside 432 adults. The sponsorship also covers the national shinty awards and the shinty and hurling international match, which Keir said is a ‘really important thing from a progression point of view’. ‘When you play for your club and represent your club at the highest level in the premiership, what is next after that? The Marine Harvest international provides the next step for the players to perform at another level.’ Shinty may have been seen historically as a man’s game, but perceptions have changed and today women are increasingly playing too, said Lisa Norman, president of the Women’s Camanachd Association. ‘The modern game is about pace, you have to be very fit and skilful and agile…if played right, it should almost be an art form.’ Women’s shinty has come on ‘massively’, said

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Shinty is played in all of the areas we farm and we are delighted to have played our part in the development of the national sport

man, growing from four or five teams playing nationally twenty years ago to around 36 now, and the number of registered female players has more than doubled from 300 in 2014 to more than 760 last year. ‘Now we’re seeing where there’s a strong shinty team, a women’s team springing up as well, which is great. ‘Marine Harvest’s funding over the last five years has made huge things possible when it comes to the development of the women’s game. They now sponsor all of our leagues and our cups and their money goes towards subsidising spaces at our development camp in the summer. ‘Without their funding, our leagues wouldn’t be where they are, our finals wouldn’t


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Community benefit – Marine Harvest

be half the occasion they are now, and just little things like if we come up with an idea –such as the development leagues - having the funding to be able to go out and pilot something has made a big difference.’ Norman said the development leagues started around three years ago: ‘We had a couple of teams come to us and say they wanted to start out but missed the start of the league and didn’t have enough numbers to enter the main leagues. So instead of saying you have to wait until next year, we just created a

Above: Strong partnership. Below: Marine Harvest Premiership 2017 winners Kinlochshiel

fun development league. ‘This has all been funded by Marine Harvest. Without their involvement a lot of these initiatives we’ve been able to come up with wouldn’t have happened. The development leagues have been key.’ Norman, who is based in Fife and has seen shinty participation grow in the Central Belt as well, said having a high profile sponsor ‘helps all of us’. ‘The name Marine Harvest and the link to shinty or women’s shinty has allowed it to be out there in the eyes of the local community and the people you want to reach.’ Steve Bracken, Marine Harvest’s business support manager, said shinty is played in all of the areas they farm and he was proud of the company’s role in developing the game. ‘When the idea of sponsoring shinty was first discussed in Marine Harvest over 30 years ago, back then, as today, we believed it had great fit with our salmon farming and processing activities in the Scottish Highlands and islands. ‘We wanted a sponsorship that would help develop the game. Quite often companies can dip in and out of sponsorships but we wanted ours to provide support over time, so that planning and development could take place and provide added financial security in the process. We are delighted to have played on the journey!’ Looking to the future, Darren Keir said the Camanachd Association’s vision is to protect and enhance shinty – and ensure it continues to be an integral part of Scottish life. ‘We’ve been able to support our clubs in the way that we do because of Marine Harvest. It’s not just the current sponsorship but the longevity of the sponsorship over a period of years. ‘It lets you plan and develop things with a little bit more clarity when you’ve got such a strong partnership. So we really value that.’

Thirty years young – anniversary marked with new youth fund

MARINE Harvest Scotland celebrated its 30 years of sponsoring shinty by establishing a Children and Young Persons Development Fund. The new agreement, with the Camanachd Association, is focused on enhancing opportunities for children and young people. The fund, launched in March, aims to increase participation at clubs by providing a maximum grant award of £500. The funding will be eligible for accredited member clubs who are proposing new or enhanced initiatives to develop shinty for children and young people, up to the age of 18. Keith Loades, the new president of the Camanachd Association, said: ‘Yet again, the sport of shinty is indebted to Marine Harvest for their generous support. ‘In this year of young people, this particular sponsorship award gives clubs with youth teams the opportunity to apply for funds to support the continued development of the game.’ 36

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The investment not only marks Marine Harvest’s 30 years of support, but also commemorates the 125th anniversary of the Camanachd Associations. Ben Hadfield, managing director of Marine Harvest (Scotland), said: ‘We are delighted to celebrate our 30 years’ support of shinty with the Children and Young Persons Fund. ‘We have been very impressed with the role the Camanachd Association has played in getting young people involved in the sport and we hope the fund will encourage even more to take part.’ Ronald Ross, regional development manager for the Camanachd Association, described the announcement as ‘fantastic news for shinty’. ‘Youth development at club level is integral to the future success of our sport and this new fund will go a long way to ensuring our young players are given opportunities that encourage them to continue their participation. ‘I look forward to continuing our partnership with Marine Harvest and ensuring shinty reaps the rewards.’ Institute of Aquaculture

08/05/2018 10:49:28

process in salmonids, hence there is significant potential for novel biomarker discovery. In a recent set of experiments we concluded that, using proteomic profiling on blood plasma, it is possible to classify steelhead trout based on their seawater readiness with high accuracy (>90%). This was achieved by using 211 molecules (protein fragments) instead of just one single biomarker. Institutethe ofpresence Aquaculture Our method increased the power of the test by not only characterising and abundance of specific molecules but also the differential ratios between them. The method itself requires a significant computational effort due to the quantity of big data generated therefore, a machine learning algorithm was used to carry out the analysis.

Rising profile

Other examples of potential applications for this approach, which is based on MALDI-TOF Mass Spectrometry, also include the rapid identification of bacteria, the identification of disease related biomarkers or the early identification of slow and fast growing fish. This work was conducted by Bernat Morro (PhD student at the Institute of Aquaculture in the University of Stirling, in partnership with his supervisors Dr Amaya Albalat ( and Dr Simon Mackenzie ( and his research partners at UniResearch (University of Bergen). Funding was provided by Lerøy Seafood Group ASA.

Proteomics as a tool for biomarker discovery in aquaculture PROTEOMICS is a developing discipline aimed at the study of all proteins present in a biological sample at a particular time. Proteomics together with other –omic technologies, such as genomics and transcriptomics, are relatively new and they have the capacity to generate, in a single experiment, a vast amount of data. The complexity of these different molecular layers increases as one moves from gene to gene transcript to protein level. Taking humans as an example, genomics would be able to identify around 20,000 genes, transcriptomics would detect more than 100,000 gene transcripts and proteomics has the potential to detect up to 250,000 to 1 million proteins. From a practical perspective, data obtained using these different technologies can then be used to compare two or more populations or experimental groups and highlight the molecular processes that explain the major differences between them. Since their appearance, all –omics technologies have steadily increased in performance and, in parallel, decreased in cost. For example, the Human Genome Project sequenced the first human genome for $2.7 billion and it took 13 years to accomplish this landmark task. Nowadays private enterprises can sequence a human genome for around $1,400 and deliver the results in weeks. These improvements have placed these revolutionary technologies at the forefront of both fundamental research and industry focused studies in biology. In aquaculture, when it comes to genomics and transcriptomics, many studies are published every year and the genomes of many farmed fish species are now available, providing a strong platform for selective breeding, for example. However, proteomic studies are still not common in the aquaculture field. Nowadays, proteomic approaches are commonly applied in human medicine studies targeting disease biomarkers. Protein biomarkers, whether based on a single protein or a group of proteins (proteomic profiling), can provide

Methodological workflow of the experiment. Blood plasma samples of seawater-ready and not seawater-ready fish were collected, analysed by mass spectrometry and data analysed with machine learning algorithms. These learned how to differentiate both kinds of fish and when presented with samples not included in the original analysis they were able to classify them according to their seawater readiness. Source: Virtual Labs

information on the early onset or progression of particular diseases allowing for early treatment therefore boosting the chances of a successful recovery. This concept is also relevant to the aquaculture industry and not only from a disease perspective. In the case of Atlantic salmon and steelhead trout aquaculture, biomarkers are used to assess the seawater readiness of the fish before they are transferred. However, predictions based on current enzymatic biomarkers only have moderate accuracy (60%), leaving significant room for improvement. But no proteomic studies have yet approached biomarker development for the smoltification process in salmonids, hence there is significant potential for novel biomarker discovery. In a recent set of experiments we concluded that, using proteomic profiling on blood plasma, it is possible to classify steelhead trout based on their seawater readiness with high accuracy (>90%). This was achieved by using 211 molecules (protein fragments) instead of just one single biomarker. Our method increased the power of the test by not only characterising the presence and abundance of specific molecules but also the differential ratios between them. The method itself requires a significant computational effort due to the quantity of big data generated, therefore a machine learning algorithm was used to carry out the analysis. Other examples of potential applications for this approach, which is based on MALDI-TOF Mass Spectrometry, also include the rapid identification of bacteria, the identification of disease related biomarkers or the early identification of slow and fast growing fish. This work was conducted by Bernat Morro (PhD student at the Institute of Aquaculture in the University of Stirling, in partnership with his supervisors Dr Amaya Albalat ( and Dr Simon Mackenzie ( and his research partners at UniResearch (University of Bergen). Funding was provided by Lerøy Seafood Group Left: Salmon parr and ASA. smolt

Improvements have placed these revolutionary technologies at the forefront of research and industry focused studies

Representative examples of the appearance of parr and smolt steelhead trout.

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08/05/2018 10:53:57

Institute of Aquaculture

Keeping time How biological clocks in ďŹ sh can help preserve health and welfare FISH have developed biological clocks, during evolution, that are synchronised to environmental changes as a consequence of geophysical cycles, such as day-night alternations, tidal cycles, lunar phases or seasons. Endogenous pacemakers play a key role in controlling fish biological rhythms, allowing them to keep time and cope with these predictable variations by anticipating recurrent events in their habitat. Chronobiology is the field of biology that studies biological rhythms, being an interdisciplinary area of research that brings together aspects of physiology, behaviour, molecular biology, ecology and evolution, among others. In the wild, fish from temperate waters synchronise their reproductive rhythms to the natural environmental cycles in order to ensure the best conditions for their offspring. Light and temperature are the most important environmental factors, acting as synchronisers of biological rhythms. Most fish adjust their daily activity patterns according to day-night and thermal cycles, so they can be classified as diurnal, nocturnal or crepuscular, when activity is linked to dawn and dusk. Melatonin, the time keeping hormone in vertebrates, is influenced by the daily cycle of illumination, being produced only at night. In this way, the synthesis of melatonin provides a calendar time to animals and regulates several biological rhythms, including reproduction. Applications of chronobiology in aquaculture Biological rhythms appear early during fish development and affect most biological functions. For this reason, the potential applications of chronobiology in aquaculture span a wide range and can help to optimise production systems and improve fish welfare in commercial facilities. In aquaculture, two key steps in the production cycle have benefited from advances in chronobiology, specifically the control of fish reproduction and larval culture. In farmed salmonids, artificially increasing day length has allowed farmers to control the timing of reproduction, overcoming the problems associated with early maturation, such as reduced growth and feed conversion efficiency. However, it is important to gain better understanding about the long-term effects of artificial light conditions on fish biology. In this context, in hatcheries, there is a need to understand how the environmental conditions can affect larval development and the onset of biological rhythms, which have important implications later during the fish life cycle. It is therefore crucial to design appropriate husbandry protocols that respect the fish physiology and behaviour, to ensure high welfare standards and an optimal growth and development of farmed fish. To achieve this, it is key to develop new technologies and light protocols that take into account the specific requirements of each species, as well as their life stage (for example, larvae, juvenile or adult). The use of new LED (light emitting diode) technologies has improved fish growth and the sustainability of the industry by reducing production times. It is essential to increase our knowledge about the effects of these new systems to determine the best illumination conditions at each stage of the production cycle, including the optimal light intensity and spectrum. In fact, different studies have revealed that fish larvae reared under a blue day-night cycle, similar to the lighting conditions in their natural habitat, grow better, have higher survival rates and present less malformations. 38

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Another promising field of application of chronobiology is the administration of licensed medicines to fish when there are outbreaks of disease. Hydrogen peroxide is one of the medicines used to control salmon louse in the UK industry. At the Institute of Aquaculture, a study was conducted into the effects of this compound on salmon stress and toxicological responses when treatments are carried out at different times of the day. The research concluded that the effects of this medicine on the fish physiology were time dependent and, consequently, the adverse effects associated to hydrogen peroxide treatments could be minimised by considering the time of the day when fish are exposed to the medicine. The aim of this strategy is to target a time window when efficiency of the treatment is optimal (increased susceptibility of the parasites to the medicine) and toxicity to the host is minimal. In aquaculture, the use of medicines is not limited to parasite control, such as sea lice infection and amoebic gill disease, but different substances need to be used at punctual times to preserve fish health and welfare, such as anaesthetics, vaccines, disinfectants and antibiotics. Nowadays, the use of functional feeds, including probiotics and immunomodulators, to enhance the immune system of fish is also gaining interest. For this reason, it is possible to find the optimal times of the day for the administration of these substances to fish, depending on when the treatments are more efficient, but the negative effects are reduced, which can lead to the optimisation of husbandry protocols in fish farms. In the case of anaesthetics, as with hydrogen peroxide, the study also found that their toxicity and effectiveness varies with the time of administration, which highlights the promising prospects for the application of this line of research in commercial facilities. In the last decade, chronobiology has showed huge Institute of Aquaculture

08/05/2018 10:55:48

Keeping time


Chronobiology has showed huge potential to overcome some of the bottlenecks affecting the aquaculture industry


Right: Biological rhythms in fish are synchronised to environmental cycles

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potential to offer innovative solutions to overcome some of the bottlenecks affecting the aquaculture industry. This can have direct benefits for production, improving economic profit, and also fish health and welfare. Consumer demand for more sustainable food and the rapid growth of the sector requires the industry to adapt quickly. Chronobiology can contribute to improving the sustainability of fish farming, which is why the Institute

of Aquaculture is leading research that will increase knowledge in this area. For further information, contact Dr Luisa Vera (luisa. or Prof Herve Migaud (hm7@ You can also read a recently published paper: Vera LM and Migaud H. (2016). Hydrogen peroxide treatment in Atlantic salmon induces stress and detoxification response in a daily manner. Chronobiology International 33: 530- 542. 39

08/05/2018 10:56:05

Institute of Aquaculture

How many light bulbs does it take to change a salmon? Potential to improve growth, reduce stress and lower sea lice infections SUNLIGHT supports almost all life on earth by providing an energy source that not only heats the planet to make it habitable, but also is the root of all our food production. However, the biological importance of light goes beyond its role in stimulating primary production of nutrients and resources. Light has a critical impact on our lives as humans. Our exposure to light can act as cues for when to sleep, when to wake up, when we feel most active, when to eat, and so on. A lack of light exposure or exposure to an unfamiliar pattern of light can have negative consequences on our body clocks, and ultimately our health. This limited or disrupted light exposure can lead to vitamin D deficiency, sleep disturbances in shift workers, seasonal depression, and jet lag for international travellers. Advances in lighting technology have made light manipulations and therapies possible. Light is also key for aquatic animals; it is used to gather information about their environment, enabling them to communicate with members of the same species, and provides clues about calendar time so they can adjust their behaviour accordingly to the seasons. Artificial lighting regimes are therefore critical in aquatic farming systems to achieve commercially desirable effects, such as faster growth and better quality food products. 40

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Research at the Institute of Aquaculture aims to characterise the biological effects of different light conditions on salmon behaviour and physiology, and determine how these lights can be applied to improve production at the different life stages. This project is a collaborative partnership with Philips Lighting, a leading international supplier of innovative aquaculture lighting systems. Two PhD students have been involved in the project, with Dr Ben Clokie focusing on freshwater lighting regimes and Lewis Warren currently looking at light during the seawater phase, both supervised by Prof Herve Migaud and Dr John Taylor. According to Dr Michiel van der Meer, R&D manager at Philips Lighting Aquaculture, ‘the work at the Institute of Aquaculture helped us to develop a product that has a big impact on the production of farmed salmon’. ‘Not only are we able to improve production by increasing the growth and reducing sexual maturation, but at the same time we can reduce stress factors in the fish and lower sea lice infections. This improves the welfare of the animals as well.’ Artificial light is routinely used throughout the salmon production cycle to alter normal behaviour and physiology, including time of ovulation in broodstock, time of transfer to sea for smolts, and control of puberty during sea on-growing. In the wild, salmon use a combination of light and temperature as environmental cues for when to transition from freshwater into seawater to increase their chances of survival post-transition. Photoperiod is also an important cue to synchronise timings of their final maturation and return to freshwater to maximise their chances of successful reproduction. However, improving the light recipe for these purposes is often focused on changing photoperiod rather than altering any other elements that make up light experienced by salmon. For the last four years, Ben Clokie has conducted research to better understand Institute of Aquaculture

08/05/2018 10:59:04

How many light bulbs does it take to change a salmon? the effects of light colour and intensity on early salmon fry development, growth and smoltification. This has shown that light experienced in freshwater can not only impact on juvenile growth and smoltification, but also have long-term effects on performances at sea. To meet consumer demand, smolt production occurs year-round, which is achieved by using photoperiod manipulation to advance or delay the smoltification process. However, a greater understanding of the influence of spectrum and intensity during this transitional change is needed to optimise the use of artificial photoperiod. Natural light available in the seas and oceans is very different to terrestrial light. As light travels down through the water column, different portions of the spectrum are more strongly absorbed, leading to some wavelengths of light that can penetrate deeper into the water compared to others. Light also loses its illuminance the deeper into the water column it travels. This creates highly variable lighting conditions in terms of spectrum and intensity. Many fish species have developed specialised vision to cope with low light intensities and limited visible col- Opposite: Sea cage lights. ours, depending on their aquatic habitat. A challenge to Below: Lights are applied the aquaculture industry is to create light regimes char- to improve production. acterised by optimal spectrum, intensity and photoperiod that most effectively stimulate a desired physiological effect in different fish species. The use of night and wintertime artificial lights in sea cages is already a useful strategy to promote growth and prevent salmon from maturing too early, and devel-

The work at the Institute helped us to develop a product that has a big impact on the production of farmed salmon

Xxxxxx_Herve Lewis.indd 41

oping gonads that spoil their fillet quality before harvest. ‘Philips Lighting customers are many times amazed by the improvements the lighting provides to the welfare and production of their salmon,’ said Dr Van der Meer. ‘We often get feedback that they eat more, because they grow faster.’ The current project undertaken by Lewis Warren aims to refine the energy efficiency and spectral range of the lighting needed to optimise this process. The project also explores the lighting requirements of triploid salmon. Previous research from the IoA has shown that triploids have different needs in terms of their diet and rearing temperature. The study is also exploring the possibility that triploids may also have basic fundamental differences in the way they perceive light. If triploid and diploid salmon are reacting differently to the same light regime this may result in both ploidies having separate lighting needs for them to perform at their best. And the research questions whether artificial lighting can do more than just manipulate the speed and timings of fish development. If the lighting and colour of the environment can affect the mood and behaviour in humans, it could be possible that different colours and intensities of light soothe stress in salmon, and could ultimately improve their health and welfare. Another interesting prospect currently being researched is the use of specialised lighting as a tool for controlling and removing sea lice. There has already been experimentation using deep water submerged coloured lights in sea cages to encourage salmon to stay away from the first few metres of the water column, where lice are most abundant, with positive results. Future research to be conducted in 2018 will further explore the use of coloured lights and their application for sea lice control. For further information on this project, please contact Lewis Warren (, Prof Migaud ( or Dr John Taylor ( jft2@stir.


08/05/2018 10:59:20

Community benefit - The Scottish Salmon Company

Pledge to our people The Scottish Salmon Company is committed to playing an active role in the communities in which it operates

WHY is Scottish salmon renowned across the world? As Scotland’s biggest food export, it is not just the taste, appearance and versatility of the product that makes it such a success, but the very fact that it is Scottish. It doesn’t take a food and drink expert to appreciate that the success of the fish, like Scotch whisky, is undoubtedly anchored in its origin, heritage and provenance. Provenance is of the uppermost importance to the Scottish Salmon Company (SSC). Operating across 60 sites on the west coast of Scotland and the Hebridean islands, SSC is the leading Scotland based producer of quality fresh Scottish salmon – and much of that success is rooted in the rural, often fragile, areas in which the salmon are raised. It is an undisputed fact that Scottish salmon is big business for Scotland. Latest official Scottish government figures indicate Scottish salmon production in 2017 was estimated to be 162,817 tonnes, with salmon the UK’s largest food export, recording sales of around £500 million each year. But the Scottish salmon industry would not be where it is today without its workforce, which is why SSC believes that its people are paramount to the robustness of its business – not only the 500 colleagues, but also those who indirectly support the work of the industry –10,000 positions in all. For many years, the Scottish Salmon Company has emphasised its commitment to investing and developing its staff and playing an active role in the communities in which it operates. The company makes no secret of its strategic focus, which is to continue sustainable business growth in Scotland by driving economic growth and enhancing value. As part of this strategy, SSC has a commitment to sourcing locally wherever possible, and in 2017 the company spent more than £100 million with 550 Scottish companies. On top of that, SSC invested over £15 million locally last year and plans to significantly increase investment in 2018, further supporting local jobs. 42

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The company’s pride and commitment in its communities is set out in its community charter, which details its pledge to work closely with people, suppliers and the communities in which it operates. The SSC also works hard to actively promote sustainable careers in aquaculture everywhere it operates. Through collaboration with national groups, including Lantra, and regional groups, including the DYW (Developing Young Workforce), as well as forging links with local schools and colleges, SSC is able to inspire young people with the diverse offerings of a career in aquaculture. SSC gives many young people a first-hand glimpse of the world of salmon farming through career talks, work experience opportunities and information events, along with attendance at career fairs. With 15% of its workforce under 25, and 12 modern apprentices recruited in 2017, the company offers them a range of sustainable careers across the supply chain, from managing production sites to becoming a human resources expert.

Institute of Aquaculture

08/05/2018 11:00:47

Pledge to our people

Salmon farming has transformed the Highlands and islands with jobs, investment and business opportunities

Recently, SSC also embarked on a new partnership with North Atlantic Fisheries College to deliver Modern Apprentices in Aquaculture. Career development is imperative to the business and, in 2015, SSC launched a pioneering professional development programme. The bespoke Aquaculture Competency Framework was initially introduced for marine and freshwater staff and is now being further developed across the company. The programme has run for two years and the company has provided a total of 9,862 hours over 42 courses. SSC’s chief executive, Craig Anderson, said: ‘Salmon farming has transformed the Scottish food sector and the rural communities across the Highlands and islands with jobs, investment and business opportunities. ‘Families are able to live and work in the communities where they were brought up, supporting the

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traditional rural way of life. ‘The passion, dedication and expertise of our staff are essential ingredients in producing the finest quality Scottish salmon and we are lucky that many of our staff have been with us for many years.’ Beyond the workplace As part of its commitment to the communities in which colleagues live and work, SSC is a proud supporter of a number of major events, including the Cowal Highland Gathering, which attracts 3,000 competitors to Dunoon in Argyll. Billed as the ‘largest, most spectacular Highland games in the world’, it combines competitions for world class pipers, dancers and athletes and attracts 23,000 visitors. It provides the perfect opportunity for the company to show its support to people who have travelled from near and far. In 2018, the company will also support the Lochcarron Highland Games and again be the main sponsor of the Isle of Skye half marathon, building on now established relationships with both events. Younger members in SSC communities also often get the opportunity to interact with the business in ways that are both educational and fun. In June 2017, schoolchildren in Uist were invited to compete to name the company’s newest work boat. Ten-year-old Sine MacLeod came up with the chosen winning name – Caileag Na Mara, Gaelic for Girl of the Sea. As well as being guests of honour at the boat’s naming ceremony, Sine and her schoolmates

Clockwise from above: Salmon papillote; the Cowal gathering; interacting with younger members of the community.


08/05/2018 11:01:04

Community benefit - The Scottish Salmon Company

received a donation for future field trips so they could learn more about salmon farming in their local community in the future. Above: Taking pride in In a further initiative, SSC will again support the Scottish provenance. National Theatre of Scotland’s Theatre in Schools Scotland programme, one of the aims of which is to bring high quality theatre to schools and school children in remote and rural areas, areas where many Scottish Salmon Company staff live and work. Following a successful schools’ tour of Jason and the Argonauts, children at Sgoil Na Parc Primary on the Isle of Lewis and at the Gigha primary school on the Isle of Gigha had a further treat when both schools won funding packages to help plan and produce their end of term shows. With SSC at the centre of many rural Scottish communities, support for groups and initiatives often comes in the form of sponsorship in kind, through donations of product and staff man hours; but colleagues do have the chance to engage in their local communities too. Through the company’s internal community fund, launched in 2017, employees can nominate local initiatives and good causes that they believe promote health and wellbeing in the community. Since its establishment, grants of up to £250 have gone towards everything from buying waterproof trousers for volunteers in the Western Isles to purchasing athletic equipment for children in Argyll and Bute. From pensioners’ groups to young people’s clubs, the Scottish Salmon Company has been able to support causes which mean the most to their colleagues. 44

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Anderson explains why having a community charter is an integral part of the Scottish Salmon Company’s success: ‘Our community charter brings our values of pride, passion and provenance to life and details our commitment to working closely with the people, suppliers and the communities where we live and work. ‘We respect our responsibility to the rural and often remote communities where we operate and where our staff live and work.’

Institute of Aquaculture

08/05/2018 11:01:24

Institute of Aquaculture

Prevention better than cure Developing vaccines against AGD in Atlantic salmon By Sandra Adams, Sophie Fridman, Giuseppe Paladini and James Bron AMOEBIC gill disease (AGD) has high economic impact in the Scottish Atlantic salmon aquaculture industry, having emerged as a problem in recent years. The disease is caused by the free-living amoeba Paramoeba perurans (Fig. 1) which is widely present in the environment. Under conditions of high water temperatures and salinity, these amoebae can attach to the gills causing lesions (Fig. 2) and respiratory distress to the fish. Unless treated, infection can ultimately lead to fish morbidity and mortality. Currently, control measures are restricted to treating fish with freshwater or hydrogen peroxide by bath immersion in cages or well-boats. This approach is expensive and logistically difficult and can have detrimental impacts on fish health and welfare. The University of Stirling is involved in two complementary projects seeking to tackle AGD through the use of vaccines. The first of these, funded by Innovate UK/BBSRC, is looking to develop an autogenous whole-cell vaccine against AGD. The second project aims to develop a recombinant protein vaccine targeting AGD. This latter forms part of the wider ParaFishControl project (, which is a €7.8 million EU funded Horizon 2020 project, involving 29 partners. It addresses the challenges of parasitic disease prevention and management in Europe, and aims to assure the sustainability and competitiveness of the European aquaculture industry. What are autogenous vaccines? Autogenous vaccines are emergency vaccines. They can be useful when new disease agents emerge and no vaccines exist, or when the pathogen is variable (antigenic variation) so that commercially available vaccines don’t work well. They are most commonly used for bacterial diseases. Isolates are collected on a given farm, the vaccine prepared and then the vaccines are used in same geographical area. We are using this approach for AGD vaccine development in collaboration with Ridgeway Biologicals. Local field isolates were collected from salmon farm sites in Scotland (Fig. 3). Clonal cultures of P. perurans have now been successfully cultured in bulk and vaccine efficacy trials are underway.

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What are recombinant vaccines? These are vaccines prepared using molecular technology (recombinant DNA technology). Before such vaccines can be produced, ‘candidate antigens/proteins’, components that can stimulate the immune response of the host animal (fish), need to be identified from the pathogen. This is the most difficult part of the process and PhD students Jadwiga Sokolowska and Carolina Fernandez, working as part of the EU ParaFishControl project, are currently working to identify promising candidates using a variety of high tech methods, such as whole genome sequencing and immunoproteomics. Once candidates have been identified, these can then be produced in high quantities artificially and used to develop vaccines. Optimising parasite vaccines Parasites are notoriously difficult to attack using vaccines, this being a result of factors such as the size and mobility of many parasites and their highly effective anti-host defences, which often specifically target the host’s immune capabilities. In addition, vaccines do not simply comprise the targeted parasite antigen, but also need additional components, termed adjuvants, to help promote a strong immune response from the host. Our current projects are therefore guided by the latest knowledge of vaccinology and host-parasite interactions in fish. This includes the research outcomes of another large EU project, Targetfish, which also involved staff from Stirling’s Institute of Aquaculture and made considerable Above: from top headway in developing new vaccine adjuvants for use Free-floating amoeba in fish. Paramoeba perurans; AGD Recent successes in targeting parasites of terrestrial on gills of Atlantic salmon farmed species provide grounds for optimism with regard to the potential for similar successes in aquaculindicated by patches ture. of white discoloration; Dr Sophie Fridman and PhD researcher Carolina Fernandez collecting gill samples and isolates of Paramoeba perurans; Photomicrograph showing amoebae on gills

Once candidates have been identified, these can then be produced in high quantities artificially


08/05/2018 11:05:37

Institute of Aquaculture

Resistance may soon become futile Understanding the genetic basis of drug resistance in sea lice SEA lice (family Caligidae) are copepod crustacean ectoparasites of marine fish, which feed on the host’s mucus, blood and skin tissues. Sea lice cause significant impacts globally as pathogens in marine finfish aquaculture, and have proven a particular problem for Atlantic salmon farming. Control of sea lice has traditionally relied on veterinary treatments delivered as medicinal baths or feed additives. In addition, non-medicinal strategies are now widely employed and include biological control using cleaner fish, thermal and freshwater delousing, and modified cage designs reducing infection pressure. Despite the accessibility of these and other new approaches to sea louse control, medicinal treatments still remain essential, as situations can arise where alternative treatment options are unavailable, are only partly successful or are advised against from a veterinary perspective. However, an inherent problem with medicinal approaches is that pests and parasites can evolve resistance against chemical control agents, particularly when the same or similarly acting compounds are used over extended time periods with insufficient rotation with dissimilar products. Resistance against drugs or pesticides is based on the increase, within the pest population, of genetic variants that allow those carrying them to survive treatments. Such genetic variants usually exist already prior to the use of a control agent, but are extremely rare within the population’s gene pool. The use of the same treatment over many generations will tend to selectively remove individuals not carrying the resistance conferring genetic variant, and therefore slowly increase its frequency in the gene pool. Once this process reaches the point where a large proportion of the parasites in a population are carriers of the genetic variants, treatment failures occur and resistance becomes apparent. Only a restricted range of anti-sea louse medicines are licensed for use in the UK. Compounds used in available bath treatments include azamethiphos, deltamethrin and hydrogen peroxide, while emamectin benzoate is used in oral treatments. The success of all the above treatments can be affected by resistance development in the salmon louse, Lepeophtheirus salmonis, the sea louse species most commonly infecting Atlantic salmon, with considerable variation of resistance occurring according to site location and seasonal/inter-annual variability. Despite the high relevance of drug resistance in L. salmonis, comparatively little is known about the molec46

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Opposite: Sea lice on salmon.

ular mechanisms involved. In insects, pesticide resistance is most commonly based on one or both of two major mechanisms. On the one hand, mutations leading to changes in the structure of the pesticide’s molecular target site can disrupt its efficacy. On the other hand, mutations increasing the breakdown of the pesticide through metabolism can enable resistant insects to rid themselves of the pesticide before it can act. In L. salmonis, resistance against azamethiphos is caused by a target site mutation. The mechanisms underlying resistance against other salmon delousing agents are currently unknown. Closing such still existing knowledge gaps with regard to the detailed mechanisms of drug resistance in salmon lice will significantly contribute to combat the aquaculture parasite. Understanding the molecular mechanism of resistance will enable the design of improved medicines capable of breaking the resistance. Moreover, the development of diagnostic tests allowing the detection of resistance in sea louse populations will allow optimising management strategies stopping the spread of resistance and monitor the success of such measures. In the BBSRC-funded research project, Identifying molecular determinants of drug susceptibility in salmon lice (Lepeophtheirus salmonis)’ (BB/L022923/1), also involving the Scottish Salmon Producers’ Organisation (SSPO), the team of Dr Armin Sturm at the University of Stirling’s Institute of Aquaculture have used a genetic approach to obtain insights into the mechanisms of resistance against the bath treatment deltamethrin and the feed additive emamectin benzoate in L. salmonis. In breeding crosses, sea lice from a population resistant against both drugs and those from a drug susceptible population were interbred and the inheritance of resistance followed through the first and second daughter generations. To identify genetic markers within the genome, which are associated with drug resistance, parasites from selected families of the crosses were subjected to high-throughput gene sequencing. The first results, summarised in a publication led by postdoctoral fellow Dr Greta Carmona-Antoñanzas (PLoS ONE, 2017, 12(7): e0180625), revealed an unexpected pattern of inheritance of deltamethrin resistance in L. salmonis. In the families obtained from cross-breeding, all offspring from resistant female parents were resistant. In contrast, whether male parents were resistant or not had only minor effects on the occurrence of deltameInstitute of Aquaculture

08/05/2018 11:06:59

Resistance may soon become futile

thrin resistance in the next generation. This maternal pattern of inheritance deviates from ‘classical’ genetic rules, as discovered by Gregor Mendel, and suggested roles of mitochondrial genes in the resistance mechanism, as these are derived from the female parent only. In support of this hypothesis, deltamethrin resistant sea louse isolates, sourced in 2012 and 2013 from different regions of Scotland, showed identical mitochondrial gene sequences, suggesting these could be responsible for the resistance, and that sea lice possessing the mitochondrial gene variant may have become dominant in populations under deltamethrin drug selection. Further research into the mechanisms of deltamethrin resistance is financially supported by Pharmaq/Zoetis. Supervised by Dr Sturm, PhD student Claudia Tschesche is performing studies aiming to elucidate the nature of the genes involved in deltamethrin resistance and to find ways of circumventing the resistance mechanism. In the above crossing experiments, inheritance of resistance against emamectin benzoate showed a very different pattern compared to that observed with deltamethrin, demonstrating that different genes are involved in the two types of resistance. With emamectin benzoate, drug susceptibility of the first daughter generation was intermediate between the susceptibilities observed in the parental generation and the numbers of resistant and susceptible parasites observed in the second daughter generation of families was in accordance with Mendelian genetic expectations. High-throughput sequencing of the genomic DNA of selected families allowed the identification and arrangement of ~5000 genetic markers distributed across the genome (called single nucleotide polymorphisms, SNPs) into a genetic map. This then allowed the identification of markers associated with resistance, highlights regions of the genome likely involved in the resistance mechanism. Ongoing research aims at identifying genes responsible for resistance in this region. When resistance problems related to emamectin

Armin Stum.indd 47

benzoate and deltamethrin were increasingly encountered, hydrogen peroxide, which had previously been used as a bath treatment in the 1990s, experienced a renaissance in use. Its increased use in recent years, associated with treatment of both sea lice and amoebic gill disease (AGD), however, raises concerns that resistance may develop. In a PhD project supervised by Dr Sturm and financially supported by Solvay, research student David Guidi is using a combination of genetic and transcriptomic methods to unravel the molecular determinants of hydrogen peroxide resistance, building upon and expanding the range of molecular tools developed in the above studies of deltamethrin and emamectin benzoate resistance. The development of resistance against a control agent leaves a characteristic footprint in the genome of a parasite population, termed a ‘selective sweep’. As discussed above, resistance is based on the enrichment within a population of genetic variants that improve survival of carriers when treated. When selection causes resistance alleles to increase in frequency, alternative variants at the same genome location will decrease in frequency. As a result, a population that has undergone drug selection for resistance will show a decrease in genetic diversity at any resistance associated genome locations and their surrounding area. Postdoctoral fellow Dr Louise Gamble is therefore currently analysing whole-genome sequencing results for sea lice collected at a number of farm sites that use different medicinal control approaches, in order to find signs of selective sweeps associated with drug resistance development. Dr Gamble is also currently re-sequencing the salmon louse genome in order to generate a better genome assembly, which will help with the process of associating genetic markers with the actual genes involved in the resistance mechanism. In summary, while there are still significant knowledge gaps regarding the mechanisms of drug resistance in salmon lice, research at the University of Stirling’s Institute of Aquaculture has identified regions in the genome of the parasite containing the resistance causing genes for deltamethrin and emamectin benzoate. Ongoing research focuses on the identification of these genes and the development of diagnostic tests allowing the sensitive detection of resistance in the field. Outcomes of the research can be expected to lead to new treatments and improved fish health management strategies for salmon farmers.

Outcomes of the research could lead to improved fish health management strategies for salmon farmers


08/05/2018 11:07:16

Institute of Aquaculture

Race to raise cleaner fish ÂŁ6.4 million invested over four years to fast-track sustainable new sector and help salmon farmers tackle sea lice challenge SEA lice are the single greatest challenge facing the modern salmon farming industry and it is not a challenge that can be faced down without a concerted pest management strategy integrating multiple control methods. To be truly effective, these management strategies must be effective, reliable, readily available and broad in their scope to combat the great capacity of the parasites to adapt and build resistance. Within this tool kit, cleaner fish have been widely hailed as a key solution, and while in principle they can be very effective, if the methodology is to work it needs to be sustainable, available to all that require it and be truly affordable at commercial scale. This is the broad challenge that the Breeding and Stock Improvement research group is seeking to address, together with colleagues in nutrition and health within multiple cleaner fish research projects. The concerted programme of research into the production and management of cleaner fish began in 2010 with a focus on ballan wrasse, with lumpfish being added to the research program in 2015.

The cleaner fish research programme at the IoA has been a true team effort, with academic leads from all the IoA research groups joining forces to offer a complete research solution to include work on broodstock management, fish physiology, nutrition, and health management, as well as cage management. This reflected the urgent need to address many knowledge gaps and fast-track the domestication process of two completely new aquaculture species. The focus in recent years has been moving towards securing and improving the breeding stocks, increasing hatchery productivity, increasing robustness of farmed animals and implementing change in the cage practices to improve and ultimately assure effective lice management using farmed cleaner fish. The two principal projects, coordinated by Prof Herve Migaud and Dr Andrew Davie, represent a major investment in cleaner fish research, with a total of ÂŁ6.5 million over four years (2015-2019) co-funded by the Scottish Aquaculture Innovation Centre (SAIC) and leading industrial partners (Marine Harvest, Scottish Sea Farms, the Scottish Salmon Company, BioMar, Pharmaq and Otter Ferry Seafish). While the cleaner fish programme is focused on delivering research, it has also proven to be very valuable for training, with many students playing a key role in performing the research. To date more than 20 MSc and BSc students have undertaken research projects within the group since 2012, often with placement in the industry. Furthermore, four PhD students have completed their doctoral research in 2015-17 and a further four are currently active within the programme. In addition, the project team has also been involved in a range of knowledge exchange activities nationally as well as internationally, with Ireland, the Faroes Islands, Norway and Canada, to assure rapid translation of findings into improved practice. Closing the lifecycle There is a strong focus on the management of the reproductive physiology for both species. Closing the


Cleaner Fish_Andrew Davie.indd 48

Institute of Aquaculture

08/05/2018 11:12:29

Race to raise cleaner fish

Opposite page: Thomas Cavrois and Samuel Pountney comparing juvenile structure using state of the art digital X-ray apparatus. Top: Wrasse vaccination. Above: Deployment size wrasse.

Cleaner Fish_Andrew Davie.indd 49

lifecycle and assuring reliable productivity from captive reared broodstocks is essential for the long-term sustainability of both species. With respect to the lumpfish, the group works closely with Otter Ferry Seafish, which had its first successful spawning of captive lumpfish broodstock in 2015. In 2016, Samuel Pountney joined the group to undertake his PhD research on the optimisation of captive broodstock management. This is not a challenge unique to the UK sector so he has taken advantage of the group’s international collaborative network and funding for trans-national access (obtained from AquaExcell) to undertake a research trial with Dr Ingrid Lein and colleagues at Nofima (Norway). The focus of the work was to define water temperature thresholds to assure good gamete quality in captive reared lumpfish broodstock. Lessons from this research, conducted in 2017, are already being implemented in the 2018 captive broodstock management plan at Otter Ferry, looking to increase the productivity and quality of future captive stock outputs. While the research into ballan wrasse has been underway for longer, closing the lifecycle in the species has been laborious due to slow growth and longer generation time. Commercial partners had the foresight to retain F1 stocks as future potential broodstock early on during the programme and the Machrihanish hatchery was proud to confirm its first mature F1 broodstock in the spring of this year. It has been a long six years from egg to mature fish and the team are a testament to the fact that fish

Optimising hatchery productivity is a key concern, given the limited marine hatchery space available in Scotland

breeding requires patience and good things come to those who wait! Going forward, the Genetics and Stock Improvement group will support the hatchery partners and develop a long-term stock management plan for the F1 animals, applying the tools and knowledge that has been generated through the collaboration over the past eight years. Assuring reliable spawning is just the first step in securing the supply of farmed cleaner fish. Optimising hatchery productivity is a key concern, given the limited marine hatchery space that is available to the sector in Scotland. This is especially true for ballan wrasse, where it currently takes in the region of 16-18 months to reach an appropriate size of animal (crica 60g) ready for deployment. It is this challenge that Thomas Cavrois is attempting to address within his current doctoral studies. He has been exploring nutritional as well as environmental 49

08/05/2018 11:12:48

Institute of Aquaculture

Opposite page: PhD student Athina Papadopolou surveying microbial communities present in ballan wrasse production. Right: Lumpsucker female broodstock; lumpsucker male broodstock.

Different degrees of delousing THE purpose of cleaner fish farming is to control sea lice and therefore the efficacy of cleaner fish at removing sea lice from the salmon hosts is critical. In the early days, cleaner fish supply to salmon farms was exclusively from the wild, and while they were shown to be very good delousers, this was not always the case. This variability in delousing activity became even more pronounced when deploying farmed cleaner fish. Dr Eric Leclercq, and more recently Dr Adam Brooker, took on the challenge to study the causes of the variability by tracking wrasse and lumpfish behaviour in salmon cages. The transfer from indoor systems under constant environmental conditions (light, feed, temperature) to open sea cages under ambient conditions was quickly identified as a cause for concern. The team therefore performed a series of trials looking at acclimation protocols in the hatchery to prepare fish prior to their transfer, transfer protocols to limit stress during their journey to the sea cages and acclimation


Cleaner Fish_Andrew Davie.indd 50

on site prior to their release into the salmon cages. The technology used is innovative in the context of fish farming, being based around hydro-acoustic monitoring, with an array of hydrophones all around the sea cage detecting the individual call sign emitted every few seconds by individual transponders implanted into the fish. This allows us to trace in real time the 3D position and movement within the cage. Results using this technology clearly demonstrated the importance of acclimation (before transfer, during transportation and on site) on wrasse behaviour, with partner farms actively changing their deployment strategy in response to this research. Many important lessons were learned while working with ballan wrasse but now the focus of the group is on lumpfish. In 2018 a large scale field trial is being initiated to characterise their behaviour when cohabiting with salmon in sea cages, to determine a set of husbandry parameters that assure optimum fish welfare and also keep delousing performance high.

approaches that could help to shorten this production cycle, while also increasing the survival of larvae and juveniles. One of his main foci has been the optimisation of live feed enrichments in order to improve early development and robustness at later stages. More recently, he explored the interaction of temperature and feed formulation on growth and digestibility in juvenile wrasse. While a balance needs to be stuck between costs and benefits, Cavrois demonstrated that optimised thermal management could result in the shortening of the production cycle by at least four months, which could have significant impact on the optimisation of hatchery facilities and comfortably offset the increased outlay of temperature management. As with all new species, understanding and thereafter effectively managing disease threats for both wrasse and lumpfish is vital in assuring the sustainability of the new industry. There are numerous health challenges currently experienced in both farmed ballan wrasse and lumpfish, therefore prioritising threats, increasing our understanding of immune function and ultimately validating effective control measures is an important area of the research activity. Based on the challenges faced in production, the management of bacterial diseases has been prioritised by the industry partners, with the long term goal being to see effective vaccines being readily available for both ballan wrasse and lumpfish. Athina Papadopoulou is a third year PhD student supported by the current project working within the health management research area. In her early work she was helping to prioritise the bacterial threats within production and through this has developed a keen focus on atypical Aeromonas salmonicida. Through the development of new typing methods she has improved our understanding of the bacterial Institute of Aquaculture

08/05/2018 11:13:07

Race to raise cleaner fish

species, which has directly helped the development and subsequent validation of an injectable autogenous vaccine that offers good protection, in collaboration with Ridgeway Biologicals.. The focus is now moving towards developing bath vaccines for small juvenile protection, but before this is possible we need to improve our understating of the development of immunocompetance in the species and that is where the current research focus is directed. Cleaner fish farming is still in its infancy, and while research is progressing rapidly with strong scientific communities in the UK and Norway collaborating together, many gaps in knowledge remain regarding the species’ biology, their environmental and nutritional requirements, their social and delousing behaviour, and their immune functions. The simultaneous domestication of two new marine aquaculture species is a significant challenge that demands sustained effort and funding over a prolonged period of time. Research must focus on enhancing the robustness of the farmed stocks (better survival in the hatchery, reduced prevalence of malformations and a disease-free status) and increasing hatchery outputs to meet the urgent demands from the salmon sector and to protect wild stocks from overfishing. The success of this innovative and unique pest management strategy will require sustained efforts for the fast-tracking of the domestication process over the next few years to ensure its sustainability and reliability and support ambitions for the expansion of the global salmon industry. For further information, please contact Prof Herve Migaud ( or Dr Andrew Davie (ad8@ Photos: Thanks to Otter Ferry Seafish

Cleaner Fish_Andrew Davie.indd 51

Genetic tools make their mark SUSTAINABILITY is a key priority and as such there has been a heavy focus for both species on successful broodstock management. From the outset it was agreed with the industry partners that domestication of the species needed to be fast-tracked so there has been a conscious effort to develop and apply genomic tools to ensure that best practice is instilled as early as possible. Dr Sarah-Louise Counter Selly has been spearheading the development and application of a range of genetic management tools for both ballan wrasse and lumpfish. An array of genetic markers have been validated and are now being used to inform management practices in the commercial hatcheries. These marker panels are being used to inform on the geographic source of founder populations,

as well as assess and subsequently manage the risk of inbreeding. In this context a landmark was reached in 2017 with the completion of genotyping of all production broodstock in the Machrihanish wrasse hatchery. More than 800 fish have now been individually genotyped and a simple guidance has been provided to the farm to ensure genetic diversity is not eroded by preventing the pairing of individuals with similar genetic profiles within the same spawning harem. The development of genetic tools for lumpfish is going one step further, with research underway in 2018 to validate the first SNP (Single Nucleotide Polymorphism) markers associated with traits of commercial interest that can be used for future selective improvement of captive farmed stocks.


08/05/2018 11:13:24

Institute of Aquaculture

Hitting the target Stirling team reports promising outcome in search for rainbow trout fry syndrome vaccine as part of Europe-wide disease prevention project

AQUACULTURE production in Europe is responsible for the employment of 100,000 people, generating an annual turnover of 7 billion EUR. However, partly due to a lack of authorised veterinary products for medicinal treatment, the consequential outbreaks of disease in farmed fish species can cost the sector up to 20% of its production value. The most appropriate method for controlling the spread of disease is to prevent it from starting in the first place, through vaccination. TARGETFISH was an EU funded project (2013-2017) which aimed to provide a long lasting contribution to the prevention of important fish diseases in the European aquaculture industry by developing fish vaccines against several bacterial and viral pathogens. Specifically, its research focused on the generation of knowledge on bacterial and viral proteins (that is, antigens), new oral systems for delivering these antigens to mucosal body sites, including the gills and gut, and new adjuvants for improving the duration of immunity. This information was then evaluated against both mucosal and systemic protective immune responses. The project aimed to develop targeted vaccination strategies and bring improved vaccines closer to industrial application by also addressing practical issues, such as efficacy, safety and delivery route. To achieve these challenging tasks for as many as six different fish species and ten different fish diseases, TARGETFISH brought together 30 partners from 11 EU member states, two associated countries and one international cooperation partner country (ICPC). Rainbow trout fry syndrome Prof Sandra Adams and Dr Rowena Hoare from the Institute of Aquaculture led the work on developing a vaccine for rainbow trout fry syndrome (RTFS) as part of TARGETFISH. RTFS is caused by the Gram-negative bacterium Flavobacterium psychrophilum, which has been respon52

Rowena.indd 52

Figure 1. a) Yellow pigmented colonies of F. psychrophilum grown on selective agar; b) typical lesions caused by F. psychrophilum; c) detection of the bacteria (brown stain) in the skin by immunohistochemistry. Figure 2. Schematic representation of stages of development for RTFS vaccine. Figure 3. Cumulative percentage survival of salmon vaccinated by intraperitoneal injection, with Flavobacterium psychrophilum formalin, killed bacterin with and without adjuvant and challenged 630 degree days post-vaccination by intramuscular injection with F. psychrophilum. Survival of each duplicate tank is shown. Average relative per cent survival (RPS): FKC: formalin-killed cells (85.71%); FKC & Squalene: formalinkilled cells emulsified with squalene and alum adjuvant (RPS 75.17%); FKC & Montanide: formalin-killed cells emulsified with Montanide ISA 760VG (RPS 95.24%).

sible for substantial economic losses in the rainbow trout industry globally for decades. The disease is widespread, occurs frequently, and can cause high mortality in fry freshwater hatcheries, but also larger fish in on-growing sites. Disease episodes tend to occur between 8-14 °C with skin lesions on the dorsal fin and tail, while in very small fish no clinical signs are apparent and death occurs due to systemic infection (Fig. 1). Recently, F. psychrophilum has also been isolated from Atlantic salmon fry in Scotland following disease outbreaks, causing concern for the industry. The use of antibiotics as a treatment for RTFS is the only option at present, highlighting the need for alternatives such as vaccines. A recent study (Verner-Jeffreys DW, Taylor NJ. Cefas 2015) of antibiotic susceptibility of F. psychrophilum within the UK revealed that the UK salmon and rainbow trout industry is critically dependent on the continued clinical efficacy of Florfenicol. Some concern must be expressed about the longterm sustainability of an industry that would be so affected by the emergence of strains of F. psychrophilum that were clinically resistant to one agent. Prior to TARGETFISH, the success of experimental vaccines against this disease had been limited. The diversity of F. psychrophilum strains and the inherent difficulties in vaccinating juvenile fish have hampered the development of a vaccine for this disease. The development of a mucosal vaccine was of primary interest to enable the vaccination of juvenile trout by immersion and this was compared to vaccination of larger trout and salmon by the intraperitoneal route (that is, by injection). Vaccine development The first step in developing the vaccine for RTFS was to determine the heterogeneity of the large collection of F. psychrophilum isolates (300+) which had been

Institute of Aquaculture

08/05/2018 11:15:32

Hitting the target

collected from clinical outbreaks in rainbow trout and salmon (1986-2015) from Scotland, England, Ireland, Europe and the US. This was done by genotyping and serotyping techniques (Ngo et al. 2017) which enabled selection of vaccine candidates with the potential for cross-protection of both trout and salmon hosts (Fig. 2). As RTFS affects salmonid fry when they are too small to vaccinate by injection, oral and immersion vaccination allows the only option for mass delivery of a vaccine to provide protection for the fish as early as possible. These methods of vaccine delivery allow mass vaccination of small fish without the need for specialist equipment or trained personnel. In order to test the efficacy of a mucosal vaccine, it is optimal to use an immersion challenge route. This more closely resembles the natural route of infection. To date, the lack of an effective and reproducible immersion challenge model has hampered the development of mucosal vaccines for F. psychrophilum. An important part of the work done in TARGETFISH was to develop an effective and reproducible immersion challenge model for F. psychrophilum. An immersion based model using hydrogen peroxide (H2O2) as a pre-treatment was recently developed by a Danish group. H2O2 accelerated the onset of mortality following immersion challenge with F. psychrophilum and increased mortality in trials up to 30%. Clinical signs corresponded to the characteristic symptoms observed in aquaculture outbreaks. The model was further developed at the IoA and mortality of over 50% was consistently achieved, which enabled efficacy testing of the novel immersion vaccine.

Rowena.indd 53


Vaccinating rainbow trout and Atlantic salmon TARGETFISH developed a prototype vaccine against RTFS. The efficacy of the new immersion vaccine for RTFS was tested in laboratory trials by immersion challenge of trout fry against two bacterial isolates not in the vaccine (heterologous); this showed promising relative per cent survival (RPS) values of 50 - 84%. Priming of the non-specific immune response was seen in head-kidney and skin of vaccinated fish and a significant increase in the mucosal antibody, IgT, was detected by expression in the hind-gut and proliferation of IgT positive cells in systemic organs of vaccinated fish. When the vaccine was applied to larger trout by the intraperitoneal route, in combination with an oil adjuvant, significant long term protection (1155 degree days) was achieved against heterologous challenge (100% RPS). This protection was strongly associated with a systemic serum antibody (IgM) response. In summary, the most promising outcome of these vaccination trials in TARGETFISH has been the significant protection observed with the application of the vaccine by immersion for rainbow trout fry against a heterologous isolate of F. psychrophilum (RPS 84%). The development of a successful immersion challenge model for F. psychrophilum has allowed appropriate efficacy testing of an immersion vaccine for RTFS. Injection delivery of the vaccine in conjunction with a traditional oil based adjuvant provided significant protection in Atlantic salmon (RPS 95.24%; Fig 3, Hoare et al. 2017) and long-term protection in rainbow trout (RPS 100%). For further information visit or contact; alexandra.adams@

Injection delivery of the vaccine in conjunction with a traditional oil based adjuvant provided significant protection in rainbow trout and Atlantic salmon



08/05/2018 11:16:11

Institute of Aquaculture

Dr Mags Crumlish, bacteriologist at the Institute of Aquaculture, said: ‘It is cr emphasise the need for more studies and collaborations between producers institutes to overcome this serious bottleneck in farming such a promising fis

Elkesh is shortly due to submit his PhD thesis describing his studies of system granulomatous disease, performed under the supervision of Crumlish and Ba Institute of Aquaculture.

Meagre mystery

This applied research received financial support from the Libyan government higher education, field support from Dr Kantham Papanna, head of veterinar Nireus S A, and supervisory support from Prof Randolph Richards. Dr Mags Crumlish, bacteriologist at the Institute of Aquaculture, said: ‘It is crucial to

emphasise the need for more studies and collaborations between producers and res

institutes to overcome this serious bottleneck in farming such a promising fish.’ To find out more, please Dr Mags Crumlish at margaret.crumlish@s Unravelling systemic granulomatous disease incontact Mediterranean farms Elkesh is shortly due to submit his PhD thesis describing his studies of systemic Johanna Baily at

MEAGRE (Argyrosomus regius) has been farmed in the Mediterranean basin since 2006, with a slowly increasing market share that reached almost 5,000 tonnes in 2016. Fast growth rates (up to 1.5kg annually), relatively easy larval rearing and a ready consumer market are all attractive features that incentivise the production of this marine finfish species. Farming a new species is never without its challenges and in 2009 reports emerged of a new disease, named systemic granulomatous disease (SGD), which spread rapidly in the Greek sector. Scientists at the University of Stirling are investigating the prevalence and cause of this disease using a variety of techniques, including histopathology, bacteriology and epidemiology. Initial diagnostic results suggested that Nocardia spp. bacteria were the cause of the disease, but research carried out since supports that the condition is less straightforward and most likely the result of multiple factors. Ahmed Elkesh, a Libyan PhD student at Stirling University, is conducting this research. ‘Following field sampling efforts, this condition was found in all sites visited, from hatchery to grow-out, in a wide range of fish sizes,’ he said. ‘By identifying risk factors for this disease, we hope to be able to help farms manage this on-going issue even if the cause remains elusive. Lower stocking densities, for example, seem to be a protective factor for this condition.’ Dr Johanna Baily, pathologist at the Institute of Aquaculture, added: ‘Histopathology is likely to prove crucial in shedding light on the progression of this disease. ‘For example, we are looking to see whether the distribution of granulomas in different tissues varies with the age of the fish, in order to better understand the progression and, ultimately, cause of this condition.’ Dr Mags Crumlish, bacteriologist at the Institute of Aquaculture, said: ‘It is crucial to emphasise the need for more studies and collaborations between producers and research institutes to overcome this serious bottleneck in farming such a promising fish.’ Elkesh is shortly due to submit his PhD thesis describing his studies of systemic granulomatous disease, performed under the supervision of Crumlish and Baily at the Institute of Aquaculture. This applied research received financial support from the Libyan government’s ministry of higher education, field support from Dr Kantham Papanna, head of vet54

Ahmed.indd 54

granulomatous disease, performed under the supervision of Crumlish and Baily at th Institute of Aquaculture.

This applied research received financial support from the Libyan government’s minis higher education, field support from Dr Kantham Papanna, head of veterinary servic Nireus S A, and supervisory support from Prof Randolph Richards.

To find out more, please contact Dr Mags Crumlish at Johanna Baily at

Figure 1: Ahmed Elkesh sampling 2 sea-winter meagre in Greece Figure 1: Ahmed Above: Ahmed Elkesh Elkesh sampling 2 sea-winter meagre in Greece

sampling 2 sea-winter meagre in Greece. Right: Typical presentation of SGD with large granulomas in the liver

erinary services at Nireus S A, and supervisory support from Prof Randolph Richards. To find out more, please contact Dr Mags Crumlish at or Dr Johanna Baily at

It is crucial for more studies to overcome this serious bottleneck in farming such a promising fish

Institute of Aquaculture

08/05/2018 11:17:37

Institute of Aquaculture

Bacteria traps Detecting a remarkable immune response that prevents infection By Andrew P. Desbois and Andre P. Van RESEARCHERS in the Institute of Aquaculture have been characterising a remarkable immune response in salmon and trout that helps to protect the fish against bacteria. The phenomenon relies on specialised immune cells, called neutrophils, unwinding the genetic material in their nucleus and releasing it in the form of a structure called a chromatin trap. The chromatin trap is a complex mesh of DNA that can entrap bacteria and prevent these micro-organisms from moving around the fish’s body to cause an infection. Once caught in the traps, it is also easier for other cells to clear up the mess and deal with the bacteria. ‘Before the traps are released from the cell, the DNA structure is decorated with compounds harmful to micro-organisms such as antimicrobial peptides (AMPs), meaning that the traps might also function to kill bacteria directly when they are captured,’ said Dr Andrew Desbois, who leads the research in Stirling. ‘A greater understanding of this immune response will uncover the role it plays in defending fish against infections. ‘This new knowledge should highlight ways we can monitor and manipulate the release of chromatin traps to reduce losses to infectious diseases in aquaculture, such as through adjusting the diet or other stock management practices.’ Since the discovery of chromatin traps in humans and other mammals, a handful of recent studies had suggested the occurrence of this response in some species of fish. However, the present work has characterised this immune mechanism in unprecedented detail to

The work required a lot of patience because many of the tools available for human and mammalian research are not available for fish

Above: Andre in the lab Left top: Fluorescent green stained chromatin traps. Left: Andre and Andrew.

Andrew Desbois.indd 55

provide a unique insight into the role it plays to protect fish against bacteria. Andre Van, a PhD student working on the project, added: ‘We used a whole range of techniques to study the structure and function of the traps. ‘The work required a lot of patience and determination because many of the tools available for human and mammalian research are not available for fish, such as the antibodies used to detect the AMPs that decorate the traps. ‘This is the first time chromatin traps have been observed in salmonids, and the molecular mechanisms of its control appear to be distinct from other species. ‘We now know much more about this immune response, but even more needs to be done to confirm their role in protecting against infections in vivo.’ Van has recently submitted a PhD thesis describing his studies of chromatin traps in rainbow trout performed under the supervision of Dr Desbois and Prof James Bron. This fundamental research on the fish immune response has also received support from the UK Research Councils, specifically BBSRC and NERC, through an award under the Sustainable Aquaculture Initiative to the Universities of Stirling, Edinburgh and St Andrews. This funding supported a post-doctoral researcher for 24 months to examine chromatin traps in Atlantic salmon. The project findings are currently being prepared for publication in a series of journal articles. To find out more, please contact Dr Andrew Desbois at or follow the publication of our articles on Twitter @DesDoesScience 55

08/05/2018 11:20:34

Institute of Aquaculture

Defence tactics Investigating what happens when a virus multiplies in trout gills GLOBAL fish production has grown steadily in the last few decades, contributing to the supply of fish and an increasing per capita consumption worldwide. This sector has a great potential to expand to meet the protein demands of the human population. However, one of the biggest challenges in aquaculture are diseases caused by viruses, bacteria or fungi. Among these pathogens, viruses are the most dominant agents that cause huge aquaculture losses. Of the ten fish diseases listed in 2016 by the OIE (World Organisation for Animal Health) as notifiable, eight are viral. Salmonid alphavirus (SAV) is one of the viral diseases causing pancreas disease and sleeping disease in farmed Atlantic salmon and rainbow trout in Europe. Six salmonid alphavirus subtypes are known and subtype 2 (SAV-2) is associated with sleeping disease, a serious infectious disease of rainbow trout in freshwater aquaculture in several European countries. Although several organs are known to be infected with SAV-2, little is known about the interaction of SAV2 and gill tissues. This is surprising since the gill is the most likely primary organ through which SAV-2 passes. In the present study, the ability of SAV-2 to multiply in trout epithelial gill cells (RTgill-w1) and the immune defence mounted by these cells was analysed. SAV-2 was found to be able to multiply in trout gill cells (RTgill-w1). The cellular integrity of the gill epithelium was found to be disturbed at an early stage of SAV2 infection. This means that the barrier of the wall like structure of the epithelium is broken, possibly allowing viruses still outside the cells to pass directly through the epithelium. However, the virus did not induce any visible changes (appearance of the cell) in trout gill cells, indicating a low level of virus multiplication. The loss of barrier function was found at the early stage of infection with SAV-2, while rebuilding of the barrier was observed at the late stage of infection. Poly(I:C), a molecule which resembles viral gene material, was found to increase the barrier strength. The trout gill cells were found to launch a strong antiviral response against SAV-2. Strong antiviral response was also observed upon stimulation with poly(I:C), which could be used to trigger antiviral defence (Figure 1). SYBR Green based quantitative PCR was used to quantify the expression of different mRNA transcripts. It is believed that microbial infection may cause leakage to the epithelial barrier. Some viruses can cause different changes to the host cell structure, such as 56

Shankar Manda.indd 56

Above: SYBR Green based quantitative PCR to quantify the expression of different mRNA transcripts.

damage to the cell cytoskeleton, which in turn can lead to breaking the cell to cell junction. This ultimately reduces the barrier strength, which can be monitored by experimental measurement of electrical resistance across the epithelium in a so called transwell. In this study, decreasing the cell barrier at an early stage of infection with higher viral concentration and recovering of the barrier at a late stage suggests a temporary partial loss of junctional integrity during early stages of virus entry. Findings of the study suggest that trout gill epithelia have the ability to mount a defence against SAV-2 infection. This also suggests that this cell defence could be induced to a greater extent by using poly(I:C) as an immunostimulant. To understand the disease mechanisms in the host cells, it is important to know host pathogen interactions. The ongoing study hopes to understand SAV-2 multiplication and antiviral defence in trout gill cells in more detail. The findings could facilitate the development of antiviral drugs/vaccines, which are conducive to aquaculture production. The study was conducted in the Institute of Aquaculture and supported by the Commonwealth Scholarship Commission in the UK. For further information, contact Shankar Mandal ( or Prof Manfred Weidman ( or Dr Simon MacKenzie (


The findings could facilitate the development of antiviral drugs/ vaccines, which are conducive to aquaculture production


Institute of Aquaculture

08/05/2018 11:23:32

Institute of Aquaculture

Gut feeling about oral vaccines How do novel strategies trigger immune response? By Sean Monaghan and Sandra Adams

VACCINATION for farmed Atlantic salmon is predominantly carried out by injection. Although very successful, this strategy has two main drawbacks: the need for individual fish vaccination and the side effects of adjuvants included in the vaccine formulations. Oral vaccination offers a number of benefits over conventional vaccination strategies as handling stress and potential adhesions are avoided. Furthermore, oral vaccination can stimulate mucosal immunity, which may be vital for protection against particular aquatic pathogens. The Institute of Aquaculture’s Immunology and Vaccinology Group has joined forces with the University of Aberdeen (UoA) and Queen’s university Belfast (QUB) to develop novel oral vaccination strategies for Atlantic salmon and to try to understand how such vaccines trigger an immune response in fish. The consortium, led by Prof Chris Secombes (UoA), includes the Agri-Food Biosciences Institute (AFBI), Tethys Aquaculture and SISAF, through which nanotechnology is being utilised to not only protect the antigen from digestion, but also control and optimise antigen release in the gastrointestinal tract (GI) of the fish. Little is known about the mechanisms by which antigen is taken up by the GI of fish following oral vaccination. We also don’t know which cells are involved or which immune responses are induced. Therefore, different regions of the GI were analysed following vaccination by different routes (injection, immersion and oral vaccination), using various bacterial (Yersinia ruckeri, Vibrio anguillarum, Aeromonas salmonicida) and viral (salmon alphavirus) vaccines as models, in Atlantic salmon and rainbow trout. Controlled oral immunisation by gavage has enabled precise analysis of antigen uptake and early responses. The results have shown differential responses throughout the GI by molecular and histological techniques whereby memory T cell-like responses can be triggered in the posterior segments of the gut (pyloric caecae and hind gut) where it is possible to target delivery and release of antigen using the applied

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nanotechnology. Whether these responses are enhancing protection compared to commercial intraperitoneal injection vaccines will soon be elucidated.

Whether these responses are enhancing protection will soon be elucidated

Above: Dissection of the different regions of the salmon GI tract to analyse differential responses. Right: Oral gavage immunisation of Atlantic salmon to study antigen uptake


08/05/2018 11:24:07

Institute of Aquaculture

Don’t get mad, get even Exploring the influence of bacterial DNA variation in sequence based fish gut microbiome studies By Christopher Payne, Mags Crumlish and Simon MacKenzie THE recent interest in how the intestinal microbial community can influence health and wellbeing has expanded to include farmed aquatic animal species, particularly finfish. These microbial communities are predominantly made of different bacterial species which together form the intestinal microbiota, and their collective genome within this environment make 58

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up the microbiome. Studies on the intestinal microbiota of farmed fish species may hold clues into understanding variation in animal growth and development, including aspects related to immunity and resistance to infectious diseases. Such evidence has been gathering for years but understanding the function of the fish gut micro-

Above: Christopher Payne analysing the number of 16s rDNA genes in rainbow trout gut samples using quantitative-PCR tools.

Institute of Aquaculture

08/05/2018 11:25:07

Don’t get mad, get even biome and how this might influence fish health has exploded recently due to access to more cost effective molecular tools. Next generation sequencing (NGS) is a molecular tool that allows analysis of DNA markers, such as the 16S ribosomal RNA gene present in all bacterial species, and has become a popular tool to investigate the abundance and composition of the intestinal microflora community in different fish species. The application of this molecular tool in aquaculture research has greatly improved our understanding of how modulation of the microflora, particularly through dietary factors, can alter the microbiome, leading to an improved gut health in farmed fish. Despite the growth of microbiome research in aquaculture, further work is required to standardise the sampling approaches in fish gut microbiome studies. Unwanted bias due to individual fish variation will compromise the ability to understand how dietary alterations can influence the gut microbiome, particularly when considering the large number of fish that are reared in production systems. No two animals will be identical in their microbiota or microbiome functions and any sampling or analysis pitfalls could distort the microbiota profile characterised, which reduces the accuracy and reproducibility of the data collected, and considerably impairs the potential of comparative studies. While technical issues, including DNA extraction and reagent contamination, have been assessed in human or animal microbiomes, the variation in gut bacterial DNA (bDNA) recovered from the intestinal tissue of individual fish has yet to be reported. Spurred on by this challenge, researchers at the Institute of Aquaculture, funded by the Fisheries Society of the British Isles, conducted a study to explore the impact of bDNA variation on the characterisation profiles of the gut microbiota in individual rainbow trout (Oncorhynchus mykiss). Researchers used NGS to compare the microflora composition and diversity between 16S ribosomal


Understanding the function of the fish gut microbiome and how this might influence fish health has exploded recently


DNA (rDNA) libraries generated using two different methods. Total DNA was extracted from the intestinal contents of six adult rainbow trout to generate 16S rDNA libraries, which represented the bacterial microbiome, using routine practices as described commonly in microbiome research. This provided genomic libraries that were generated using total DNA concentration, and also included the DNA from the fish and other non-bacterial (viral or fungal) DNA which are common contaminants in fish microbiome samples. An aliquot of the original DNA samples was then optimised to reduce unwanted DNA by measuring the number of bacterial only (16S rDNA) genes using a quantitative PCR (q-PCR) approach (figure 1). q-PCR values were used to accurately estimate the bDNA content, so that each optimised 16s rDNA library was adjusted to equal template bDNA. All libraries were then processed on the Illumina Miseq to characterise the 16s rDNA microbiome in each gut sample. The results from the qPCR analysis showed that the amount of bDNA recovered from intestinal samples varied significantly between individual fish as the average number of 16s rDNA genes recovered from fish samples ranged from 107 and 109 copies per g of intestinal contents. Researchers also demonstrated through gel electrophoresis, that the optimised preparation enabled a more uniform amplification of the 16s rDNA marker gene between samples when compared with the traditional method (figure 2). Future work is now focused on understanding the influence of bDNA variation when performing gut microbiome characterisation in teleost fish using associated computational methods. Building on these findings, researchers hope this study will provide an improved preparation protocol for NGS of fish intestinal samples, thus generating more accurate profiles of the microbiota community in microbiome studies. Uptake of these methods would promote better comparative analysis between different studies and help to advance fish microbiome research in the future. For further information, please contact Christopher Payne (c.j.payne1@stir. or Dr Mags Crumlish ( or Dr Simon MacKenzie (

Above: Agarose gel electrophoresis of 16s rDNA gene in rainbow trout gut contents. Lanes 1-6; 16s rDNA libraries from six individual rainbow trout generated using the optimised method. Lanes 7-12; 16s rDNA libraries generated using traditional methods. Lane 13; DNA from a mock microbial community (positive control). Lane 14; No DNA (negative control).

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08/05/2018 11:25:30

Community benefit - Grieg Seafood

Local lifeline From football to festivals to wild fishing - salmon farmer Grieg Seafood supports the people of Shetland and Skye BOTH at home and abroad, consumers love Scottish salmon for its taste, quality and provenance, making it Scotland’s and the UK’s top food export. The industry is a key part of Scotland’s economy and in just 40 years has transformed the domestic food sector and the remote communities of the Highlands and islands, with investment, business opportunities and year-round stable employment. Salmon farming supports 10,340 jobs in Scotland, provides earnings of £270 million per annum and, crucially, benefits around 3,500 Scottish companies which are doing business with salmon farmers. In fact, second generations are now joining the sector, attracted by the modern apprenticeships, training opportunities, and the impressive choice of jobs, which range from engineers to technicians, from marketing to sales. In addition to the financial benefits, the industry is committed to supporting the local communities where staff and their families live and work. Grieg Seafood (Shetland) is a prime example of this ethos. One of the world’s leading fish farming companies, Grieg operates 18 salmon farming sites in Shetland Grieg also provided vital sponsorship for the Shetland Table Tennis Association to and the Isle of Skye, and during 2017 donated almost send a team to the high profile NatWest International Island Games on the Swedish £70,000 to support local clubs, organisations, events Island of Gotland. and projects across both locations. Shetland Golf Club received a boost to its Summer League Competition, with further awards to the Shetland Football Works League and the Shetland Amateur Community is key Athletics Club. Last year, nine cash awards underlined the company’s Other clubs and organisations to benefit from Grieg’s community fund included commitment to promoting and encouraging sporting the Whalsay Model Yacht Club and the Zetland Motorcycle Club (ZMCC). The latter activities and opportunities for all ages and abilities. organisation has been running since 1930 and is an eclectic mix of bikers based in The Shetland Darts Association, North West Skye Shetland. Amateur Football Club, Shetland Junior Football AssoThe club prides itself on including all bikers, from 50cc’s up to 2300cc’s, and has ciation, Shetland Kung Fu and Kickboxing Association travelled south to three rallies, at which members won trophies for furthest travelled and Enertec Racing Team all benefited from financial club, biggest turn out and best bike. support. During 2017, Disability Shetland also received Grieg’s backing to support its efforts to assist disabled people to realise their full potential in all areas of life, while Scalloway Preschool welcomed funding from the company for its work in creating a caring, homely and friendly place for children to play and learn. Lifesaving boost Grieg’s ongoing commitment to community safety was demonstrated by its successful collaboration with the lucky2bhere project to install defibrillators on all Grieg’s shore bases on Skye. Lucky2Bhere was established in 2007 by local man Ross Cowie, who survived a heart attack thanks to lifesaving equipment in a nearby ambulance. As a result of his experience, he raised funds to purchase a defibrillator for the Skye Camanachd Shinty Club in Portree. From these beginnings, L2BH is now a registered charity which provides defibrillators and emergency life support training on Skye and throughout Scotland. Grieg also supports the vital work of Shetland Coastguard, which patrols the 1,697 miles of Shetland shoreline and a sea area of 43,840 square nautical miles. 60

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Institute of Aquaculture

08/05/2018 11:27:27

Local lifeline

Nine cash awards underlined the company’s commitment to promoting and encouraging sporting activities

Festival sponsorship Elsewhere, Grieg was one of the core sponsors of the 37th Shetland Folk Festival, which attracted a record 7,500 concert goers to the weekend event. The company also lent its financial backing to Up Helly Aa, the world famous Viking themed festival which takes place in Lerwick on the last Tuesday in January every year and involves a series of marches and visitations, culminating in a torch-lit procession and the burning of a galley. As you would expect from a world class food producer, Grieg supported the work of Shetland Food and Drink, a membership organisation which represents leading producers and proudly promotes the islands’ wonderful produce to the world. Meanwhile, 2016-17 saw particularly strong exam results for those studying English for Speakers of Other

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Clockwise from top: Grieg Seafood operates farming sites in Shetland and Skye, where it promotes a range of community projects.

Languages (ESOL) courses at Shetland College UHI. Classes are delivered at a range of levels to meet the needs of individual students, with support provided to help improve speaking, listening, writing and reading skills. In recognition of the fact that around 20 per cent of Grieg Seafood Shetland’s employees are EU nationals, the company sponsored the class prize for top English language student, which was won by Monika Lis, who moved from Poland to Shetland with her family in 2014. Closer co-operation Grieg is also working hard to forge closer bonds with the wild fishing sector. To this end, the company funded an innovative joint project with the University of Glasgow and the Skye and Wester Ross Fisheries Trust to sponsor a PhD student at the Scottish Centre for Ecology and the Natural Environment. Isabel Moore is researching the health of wild sea trout populations in Skye, and Grieg is sponsoring her work to the tune of £30,000 per annum. Grant Cumming, managing director Grieg Seafood Shetland, has welcomed this collaboration with the wild fishing sector. 61

08/05/2018 11:27:48

Community benefit - Grieg Seafood

• Inter-company co-operation - more demanding farm management agreements with other neighbouring operators, placing an emphasis on synchronous fallowing and close working cooperation; • Sea lice skirts - tarpaulins which surround the top six metres of the salmon pens and help to prevent the planktonic stage of the sea lice from encountering and settling on its salmon; • Cleaner fish programme - culturing lumpsuckers (Cyclopterus lumpus) which eat the lice from salmon. Going forward, the company plans to stock lumpsuckers on all sites. Grieg is not using wild caught cleaner fish; • Aeration systems - designed to draw deep water up to the surface in the net pens. This system can help to keep algae and jellyfish, as well as planktonic sea lice, away from salmon. This will reduce sea lice infection rates and improve the gill health of the salmon; • Freshwater treatments for sea lice - Grieg has the capacity to treat fish with freshwater. This is effective at controlling Amoebic Gill Disease and sea lice. It also reduces reliance on sea lice medicines.

He said: ‘Grieg is delighted to be able to partner with the University of Glasgow and Skye Fisheries Trust to sponsor Isabel Moore’s PhD research project. ‘This is an unprecedented opportunity to study the health of Skye’s wild sea trout population and share the information within the industry. ‘Salmonid numbers can be affected by a number of factors, including river management measures, deforestation, sea lice abundance, and increased rainfall intensity. ‘There is also the issue of global warming and ocean acidification that may be affecting prey availability in the sea and breeding success in our rivers. ‘However, it is clear that as a responsible industry we must do our bit to reduce the impact we may have on wild fish runs. ‘It is in the interest of both the wild and farmed fish sectors to co-operate as sustainable salmon farming and the wild fishery industry both brings enormous benefits to Scotland.’ Industry challenges Rising seawater temperatures and the emergence of new diseases, such as amoebic gill disease, have challenged the industry recently. This, together with reduced sensitivity to sea lice medicines, has made it harder to control sea lice numbers. These challenges have led to considerable investment and innovation within the industry, leading Grieg to explore fresh solutions to both old and new problems. Cumming continued: ‘Grieg has cut production and increased fallow periods (the length of time sites remain empty after harvesting the fish prior to restocking) to allow the company to get on top of these challenges in as short a timeframe as possible. ‘We have cut our harvest biomass from a peak of 19,723 tonnes in 2015 to a low of 12,055 tonnes in 2017. We plan to harvest a similar amount in 2018. This is a proactive, sustainable and pragmatic approach to these challenges.’ Grieg Seafood (Shetland) has invested in the following control methods to help maximise survival: 62

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Above: The company not only provides local jobs but supports rural initiatives.

Cumming concluded: ‘While these changes, many of which have been introduced at a commercial scale in the last year, still need time to fully demonstrate their effectiveness, we are very encouraged by early results. ‘At the end of March 2018, Grieg Seafood’s total salmon lice numbers per fish were reduced by 83 per cent when compared to the figures for the end of March 2017. Adult female salmon louse numbers were reduced by 87 per cent on the previous year.’

Institute of Aquaculture

08/05/2018 11:28:11

Institute of Aquaculture

Bigger picture How environmentally responsible is IMTA? By Steven Prescott

Above: Mussels

ENVIRONMENTALLY sustainable food production is a hot topic with huge public appeal. Conversely, fish farming has had considerable negative publicity and so is keen to enhance its environmental credentials by being associated with sustainable practices, such as integrated multi-trophic aquaculture or IMTA for short. But how environmentally responsible is IMTA? The basic environmental goals are to reduce the overall nutrient load entering the sea from fish farms by growing mussels or seaweed nearby, which use these nutrients as food. An intuitively sustainable approach? Most publications agree so. There have even been suggestions of government subsidies and eco-labels for farmers who adopt this approach; the salmon produced in this way might gain an edge in terms of market appeal. But, the question is: ‘Does IMTA really represent a more sustainable way of farming fish?’ This is not easy to answer, but there is a way of gaining further insights. Firstly, we must acknowledge that we cannot determine the sustainability of a farmed product, such as salmon, by focusing only on the activities of the farm; we must also consider the entire production chain that goes before it. This means we need to calculate the environmental impacts of feed ingredients, such as agricultural crops and fishmeal, and of the extraction and use of fuels, such as diesel. We must also acknowledge that a product has multiple potential environmental impacts, including impacts resulting from nutrients entering the sea. And we must consider other sources of pollution, such as those which damage soils, contribute to global warming, or rely on unsustainable supplies of fossil fuels. This presents a complex picture, but its analysis is made possible by Life Cycle Assessment (LCA). LCA

We cannot determine the sustainability of a farmed product, such as salmon, by focusing only on the activities of the farm

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allows us to estimate the quantitative contribution towards a variety of environmental impacts, of each activity within a production chain. The complexity of food production systems means that LCA cannot always provide absolute answers from a numerical point of view. Nevertheless, its ability to describe food systems within the broad context of sustainability is without equal, and essential for answering our question. Drawing from a joint LCA project between the Chilean i-mar Centre of Investigation, and the Institute of Aquaculture, we can make some general conclusions. IMTA has lower nutrient emissions than a typical salmon monoculture, but this can occur at the expense of an increased contribution to other environmental impacts. The balance of these trade-offs may be optimised by altering the ratio between the different crops. But what impacts should be given priority? When nutrient enrichment is a problem, this might favour IMTA. But otherwise, IMTA may increase contributions to some environmental impacts without a definite justification. Of course, the issues are much more complicated than this, but even the existence of these general issues make it apparent that it is too soon to promote IMTA as a sustainable alternative to fish monoculture. Clearly, we need to think about fish production in a broader lifecycle perspective to gauge overall sustainability. And this goes for all food products, not just fish. 63

08/05/2018 11:30:24

Institute of Aquaculture

Time for TAPAS? Better planning will promote growth in the European aquaculture sector By Lynne Falconer and Trevor Telfer DESPITE increased demand for seafood, in many European countries aquaculture growth has slowed or stagnated. Several factors are thought to have contributed to this, but lack of space and inconsistent regulatory frameworks are considered to be the main bottlenecks to further development. Aquaculture is one of many activities competing for space and resources, so potential areas for sites are limited. And even if an area is available for development, it may not be suitable; aquaculture species and systems have specific biological and environmental requirements that must be met, as well as other social and economic considerations that are necessary for a viable business. One of the main challenges then is to identify locations that are available for aquaculture development, and then optimise the use of the space and resources. Appropriate regulation and policy is key to aquaculture development and governance, but although mechanisms exist in most countries, implementation and approaches are inconsistent and the legislative and administrative processes can be complicated, as well as time consuming, for industry and regulators. Often, stakeholders lack the necessary tools and information to make decisions, leading to delays or uncertainty about a planning application or a regulatory issue. Furthermore, many of the regulatory and licensing processes lack transparency, which can result in confusion and affect public perception of the industry. Thus, there is a need to implement more flexible and transparent, cost efficient licensing approaches that are supported by models and tools to assist both aquaculture producers and regulators in identifying suitable sites and levels of production, both for future development and managing existing sites sustainably throughout Europe. Tools for Assessment and Planning of Aquaculture Sustainability (TAPAS) is a fouryear, â‚Ź7 million EU Horizon 2020 funded project. It started in 2016 with the aim of developing and recommending improved approaches to policy and governance, together with tools, models and frameworks to support transparent and efficient licensing that can enhance environment sustainability, aquatic food security and blue growth. Covering the key production systems throughout Europe, including freshwater ponds, re-circulating systems, shellfish farms, marine cages, and emerging technologies such as integrated multi-trophic aquaculture (IMTA), the project uses a combination of field work, lab work, computer based modelling, policy reviews and stakeholder consultation to develop approaches to strengthen planning and management strategies. The major planned outcome of TAPAS is the development of an aquaculture sustainability toolbox and flexible decision support framework, designed to facilitate efficient planning, regulation and management of aquaculture. Coordinated by Prof Trevor Telfer at the Institute of Aquaculture, the project consortium has 15 partner organisations from 10 countries across Europe, including research institutions, SMEs, regulators and aquaculture certifiers. The team at the Institute of Aquaculture also includes Dr Lynne Falconer, who leads the cross-partner research on ‘Near field models for regulation and site selection’, and PhD students Akpojotor Ekpeki, Anastasios Baltadakis and Karl Cutajar, who are working on improved models for freshwater and marine systems. Two years into the project, having just passed the half-way milestone, the main licensing and regulatory issues affecting marine and freshwater aquaculture in Europe have been identified and initial evaluation of existing models, tools and approaches used has been completed. 64

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An important concept within the project is to avoid reinventing the wheel, so an important step has been to look for examples of best practice that could be used or adapted for other countries and/or aquaculture production systems. Where gaps and limitations have been identified, improved and new approaches are being developed. At farm and water body scale, this includes models for site selection, carrying capacity, production potential and ecotoxicological risk assessment. Regional scale assessments for the North Atlantic, Mediterranean and Baltic Sea are producing maps of risks and opportunities for aquaculture which could support pan-European strategies for sustainable growth. TAPAS is also considering combined environmental and social impacts, so work is underway to develop and test an analytical framework for assessment of ecosystems services and ecosystem services trade-offs from aquaculture that can be incorporated into planning and licensing processes. Data collection and environmental monitoring is an important part of licensing, regulation and management of aquaculture. New in-situ real time surveillance technologies are therefore under development and currently being tested in the field, including an autonomous underwater vehicle (AUV) for cage net inspection and optical sensors for observations of water quality. In line with the aim of improvement in governance across Europe, a draft report on new and flexible approaches for licensing has been prepared in advance of a series of stakeholder meetings which will take place over the next year. The report, compiled by project partner the Marine Institute Ireland, highlights the main issues uncovered after an in-depth pan-European stakeholder consultation, and makes recommendations and suggestions that could facilitate more timely and cost efficient licensing. At Stirling, much of the research is focused on near field models for marine and freshwater environments. Several models already exist for marine cage culture and these are being evaluated and tested under a range of conditions and case study locations throughout Europe. Included in this is adapting near field models for IMTA which are currently being tested on pilot scale systems in Ireland and Malta. The models are being developed to optimise available space, assess nutrient transfer between species and estimate the production Institute of Aquaculture

08/05/2018 11:32:40

Time for TAPAS?

potential of the system as a whole. For freshwater systems, attention is focused on developing improved carrying capacity models that are being tested at Scottish lochs used for salmonid culture, extensive pond systems in Hungary used for carp culture, and recirculating systems for trout production in Denmark. The aim is to enable more transparent approaches for setting biomass limits and supporting planning applications and licensing. Near field models and their use for regulation are only effective for managing sites which are suitable for aquaculture in the first place. This is important when balancing the conflicting pressures of the aquatic environment and the environmental quality needs for efficient and sustainable aquaculture production. Therefore, a major part of the project is the development of a spatial framework for regulation and site selection. Stirling researchers are working with TAPAS partner DHI ( to develop an approach using Geographic Information Systems (GIS) that can be used by stakeholders to identify suitable locations for freshwater and marine aquaculture. This site selection framework will consider the availability and suitability of the environment for aquaculture. DHI is also responsible for developing the decision support system and Aquaculture Sustainability Toolbox, which will include near and far field models for nutrient and chemical exposure and effect, guidance documents and examples of best practice for effective licensing, regulation and governance of aquaculture throughout Europe. The next two years will be a busy and exciting time for the TAPAS consortium as tools and approaches are finalised and integrated within the Aquaculture Sustainability Toolbox and then tested using a number of case studies. The project will also make policy recommendations which demonstrate the approaches that can be used to overcome the previously identified bottlenecks, encourage sustainable development and enhance the public image of the sector. Stakeholder engagement is also a key part of the project as it is important to ensure the approaches

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The use of appropriate tools and approaches can help the industry make more informed choices

Above: The team meet in Malta; Stirling PhD student Akpojotor Ekpeki. Below: Dr Lynne Falconer and PhD student Anastasios Baltadakis.


being developed and suggested are relevant and useful to industry and regulators. A series of formal and informal events aim to facilitate discussions and consultations on the project and its outputs. TAPAS is a timely project that addresses some of the key issues affecting the sustainable development of the aquaculture industry in Europe. Many of the issues are due to unsuitable sites and poor planning, so the use of appropriate tools and approaches can help decision makers and industry make more informed choices and alleviate some of the bottlenecks that have slowed the sustainable growth of the sector. The TAPAS (Tools for Assessment and Planning of Aquaculture Sustainability) project has received funding from the European Union Horizon 2020 Programme under grant agreement No. 678396. For more information, visit and @tapas_h2020. Or contact Dr Lynne Falconer ( or Professor Trevor Telfer (


08/05/2018 11:33:00

Global reach - WorldFish

Feeding the


Research programme underlines growing significance of fish within the food system THE United Nation’s sustainable development goals (SDGs) will not be achieved if we do not take into account the power of aquaculture and fisheries to positively affect livelihoods, food and nutrition security. Fisheries and aquaculture contribute to the livelihoods of 800 million people and provide 3.2 billion people with 20% of their animal protein, as well as micronutrients and essential fatty acids critical to cognitive and physical development. Three-quarters of the countries where fish contributes more than one-third of animal protein in the diet are low income, food deficit countries, where fish is often the cheapest and most accessible animal source food. To meet the future demand for fish, in many countries of Africa and Asia supply will need to double or more by 2030. The CGIAR research programme on fish - FISH - is a response to the challenges and opportunities for sustainable aquaculture and wild fisheries systems within the developing world. The CGIAR is a global research partnership for a food secure future, dedicated to reducing poverty, enhancing food and nutrition security, and improving natural resources. The new FISH programme within its portfolio is a strong recognition of the growing significance of fish within the world food system. The six-year (2016-2022) programme aims to sustainably improve the productivity of aquaculture and fisheries and enhance the contribution of fish to global development goals. WorldFish leads the programme, together with the International Water Management Institute (IWMI) and three advanced research institutes: the Aquaculture and Fisheries Group at Wageningen University (WUR), the Australian Research Council Centre of Excellence in Coral Reef Studies at James Cook University (JCU), and the Natural


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Resources Institute at the University of Greenwich (NRI). A number of research institutes and development NGOs that work globally played a key role in FISH’s programme design and are central to its implementation. The University of Stirling is a partner to this initiative, contributing research expertise across genetics, fish nutrition, health and aquaculture systems. Other leading UK research institutes, including the Roslin Institute, University of Exeter and CEFAS, are also playing important roles in this expanding and unique scheme. The FISH programme works in Africa, Asia and the Pacific. Country selection is based on demand from partners and the potential for impact, in locations where fisheries and aquaculture makes a significant contribution to animal source food supply, and where the potential to contribute to better livelihoods and address food and nutrition insecurity challenges is high. Research is presently directed towards six focal countries (Bangladesh, Cambodia, Myanmar, Nigeria, Tanzania and Zambia) and two hub countries (Egypt and Solomon Islands). Successes and lessons learned from research will be scaled to achieve impact, and expanded, initially with a focus on Ghana, India, Indonesia, Kenya, Philippines, Malawi and Vietnam. Research agenda The project has a goal to increase socially (and gender) inclusive production and the equitable distribution of nutritious fish to those most in need. The research focuses on the two interlinked challenges of sustainable production from aquaculture and small-scale fisheries, with cross cutting themes of gender, youth, climate change and nutrition. It will look at enhancing the contribution of aquaculture to poverty reduction, food and nutrition security and natural resource management. The research has three major research clusters: fish breeds and genetics; fish health and nutrition; and aquaculture systems. Fish breeds and genetics research aims to enhance the production efficiency and sustainability of tilapia and carp farming systems. It will focus on applying new genomics tools to identification and selection of new traits, with a particular interest in tolerance to disease, feed efficiencies and applying concepts of ‘resilience’ to improved fish breeds. The core genetic improvement programmes with Nile tilapia are based in Malaysia and Egypt, with a new genetic improvement programme for carp in Bangladesh. Carps make up the majority of aquaculture production within South Asia, with significant opportunities for improvement. Institute of Aquaculture

08/05/2018 11:34:00

Feeding the world


To meet future demand, in many countries of Africa and Asia supply will need to double or more by 2030


A foundation is also being laid for a new long-term genetic improvement programme in Zambia with Oreochromis andersonii, in partnership with the Department of Fisheries Zambia, and in Malawi with partners for the upgrading of an existing O. shiranus genetic improvement programme. At the same time, support is being provided to various national projects in Africa, Asia and the Pacific, involving a mix of public and private partners. These will enhance the efficiency of breeding programmes and facilitate the dissemination of improved fish seed to small-scale farmers, with national partners in Bangladesh, Cambodia, India, Myanmar and Timor Leste. Fish health research is being given increasing attention in FISH, with a focus on tilapia health and solutions to the management of the tilapia lake virus (TiLV), a newly emerging fish disease problem with global implications. The programme is involved with epidemiological assessments in key producing countries in Africa and Asia, development of diagnostic techniques accessible for small-scale farmers, and wide dissemination of better health management practices with public and private partners. The fish nutrition work, complementary to the genetics and health research, investigates the identification and application of novel feed ingredients, particularly for the replacement of fish meal and oils, improvement in feeding efficiencies, and reduction in reliance on

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human food crops for fish feed. Aquaculture systems research involves a spectrum of research, from design of low carbon footprint and water efficient production models, packaging of technology and best practices for sustainable intensification and enhanced adaptive capacity, to climate risk, identification of gender sensitive approaches to aquaculture and the development of business and entrepreneurial models for small-scale farmers. The programme is also gathering a unique collection of models, data and analytical capacity that will be used assess performance and adoption of aquaculture technology innovations, in close cooperation with a CGIAR platform on big data. Impact assessment and foresight modelling, linking fish production, consumption and trade, are also being used to generate knowledge to guide policies and priorities for civil society, development and government agencies. Apart from aquaculture, the FISH programme also gives attention to small-scale fisheries research. A recently launched Hidden Harvest study, with the FAO and partners, seeks to highlight the importance of small-scale fisheries in the livelihoods and food and nutrition security of many millions of people throughout the developing world. Research aims to improve the resilience of coastal marine fisheries, the management of small-scale fisheries in complex landscapes, particularly rice dominated landscapes in Africa and Asia, and generate new knowledge and understanding of the role of small-scale fisheries within regional food systems. FISH is a collaborative global partnership to sustainably improve the productivity of aquaculture and fisheries and enhance the contribution of fish to global development goals. FISH runs from 2016-2022, with a focus on countries in Africa, Asia and the Pacific. For more information, contact Dr Michael Phillips, FISH Director or 67

08/05/2018 11:34:18

Institute of Aquaculture

Forecast 2050 Impact of climate change on European seafood production By Trevor Telfer, Lynne Falconer and Bruce McAdam CLIMATE change is linked to public health, food and water security, migration, peace, and security, said the then United Nations secretary-general Ban Ki-moon in 2016. ‘It is a moral issue. It is an issue of social justice, human rights and fundamental ethics. We have a profound responsibility to the fragile web of life on this earth, and to this generation and those that will follow.’ Aquaculture is the fastest developing food production sector on the planet but how it is affected by climate change is poorly understood. The vulnerability of aquaculture production and associated livelihoods varies significantly throughout the world. It is likely to be greatest in Asia for freshwater and brackish water production, but in some parts of Europe and South America for marine production (Handisyde et al, 2017, doi: 10.1111/faf.12186). ClimeFish is a European Horizon 2020 funded project, running from 2016 to 2020, which is investigating the impact of climate change on seafood production throughout the European Economic Area from now until 2050. Coordinated by the University of Tromsø, the project’s 21 partners, in association with stakeholders, plan to co-create models to forecast the effects of climate change sustainability on wild capture and cultured European seafood to 2050. Consequently, a constructed decision support system will enable the implementation of management plans in line with the ecosystem approach to allow European regulators, fishers and aquaculture operators to anticipate, prepare and adapt to climate change, while minimising economic losses and social consequences. The Environmental Management Research Team of the Institute of Aquaculture, as one of the project partners, is developing forecasting models of the effects of climate change on Atlantic salmon and shellfish grown in Scotland and Norway. Using model outputs of climate change projections, produced by the Institute of Marine Research in Norway (see Figure), growth forecasting models for Atlantic salmon have been formulated. These combine the outputs from the Ewos EGI model (Cargill Inc) with a newly developed dynamic energy budget (DEB) approach. Nofima and the Institute of Aquaculture are now using these models as part of a north-east Atlantic case study for Atlantic salmon, using farm level data throughout Scotland and Norway. The preliminary models were presented to stakeholders are a meeting in Oslo in April and we are now working with both Scottish and Norwegian salmon industries to further refine them. Early results show that there are both advantages and disadvantages to the changing sea surface properties 68

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Above: The ClimeFish partners at the first annual meeting in Crete, 2017.

Early results show there are both advantages and disadvantages for the salmon industry

for the salmon industry, especially in the wide temperature ranges between southern and northern Norway. As another part of this initiative, ClimeFish and CERES, a parallel H2020 project on the effects of climate change on aquatic production, are contributing to Seafish’s Climate Change Adaption Plan for Aquaculture in the UK. Climate change risk matrices, which are the foundation to the report, have been compiled jointly between Seafish, CEFAS, the Institute of Aquaculture and the Scottish Salmon Producers Organisation and are now under further consultation with stakeholders before finalising. See and ClimeFish for more information. This project has received funding from the European Union Horizon 2020 Programme under grant agreement no. 677039.For more information, contact Trevor Telfer (, Lynne Falconer (lynne. or Bruce McAdam (b.j.mcadam@

Institute of Aquaculture

08/05/2018 11:35:28

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On the Horizon Stirling leads large, EU funded research initiative By Dimitar Taskov and Francis Murray A PROJECT to enhance the economic sustainability and competitiveness of European fisheries and aquaculture brings together expertise from across Europe, Canada and Vietnam. Stirling University’s Dr Francis Murray, John Bostock and Dimitar Taskov, in collaboration with their international colleagues, lead on the value chain analysis and competitiveness work package within the multi-disciplinary EU Horizon 2020 funded research project, Primefish. The overall objective of PrimeFish is to enhance European fisheries and aquaculture sectors in light of the increasingly globalising seafood supply and associated competitive pressures for the European seafood producers. A central part of the project, involving leading universities and research organisations, is the development of a ‘decision support toolbox’. This will consist of interactive applications designed to help seafood businesses and policy makers improve their understanding of the functioning of markets - and enable them to establish strategic plans for future production and innovation. Stirling’s contribution to this work includes a value chain analyser tool comprising a market structure visualisation, industry report generator, value calculator and certification mapping functionalities. For more information, visit, or contact Dr Francis Murray (

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Above: PrimeFish meeting at Stirling University. From left to right: Francis Murray (Stirling University), Ray Hayter (Memorial University, Canada), Jose Santiago (CETMAR, Spain), Ögmundur Knútsson (University of Iceland, Iceland), Paul Steinar Valle (Kontali Analyse AS. Norway), Heather Manuel (Memorial University, Canada), Sveinn Agnarsson (University of Iceland), John Isaksen (Nofima, Norway), Ólavur Gregersen (Syntesa, Faroe Islands), Valur Gunnlaugsson (Matis, Iceland), Oystein Hermansen (Nofima), Gudmundur Stefansson (Matis), Dimitar Taskov (Stirling University), Søren Qvist Eliasen (University of Aalborg, Denmark), Andrew Baxter (Syntesa, Spain), Annika Gering (TTZ Bremerhaven, Germany), Olga Untilov (University of Savoie, France), John Bostock (University of Stirling).

A central part of the project is the development of a decision support toolbox


08/05/2018 11:37:32

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Top of the crops SNIPH-ing out new sources of omega-3 By William D. Clark AS the beneficial effects of consuming omega-3 fatty acids are well known, it is an unfortunate fact of our global economy that access to this key essential nutrient is often largely determined by socio-economic status. This is certainly the case in India and East Africa, where populations have been identified as having low or very low omega-3 status, with associated consequences for individual and public health. A project to address this dietary and social imbalance in an ethical, sustainable and environmentally sensitive way is being coordinated by the Institute of Aquaculture. ‘Development of alternative sustainable fish feeds to promote human health using novel non-conventional indigenous ingredients’, or ‘Sustainable New Ingredients to Promote Health (SNIPH)’ for short, is funded by the BBSRC Newton Fund Global Research Partnership (GRP). Appropriate dietary amounts of the omega-3 polyunsaturated fatty acids (PUFA) -eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) - are critically important to maintaining human health and preventing chronic disease. These fatty acids are essentially only made in the marine environment and so fish and seafood are the main sources in our diet. To access the beneficial effect of omega-3, recommendations (500mg per day) equate to two servings of oily fish per week. However, even at the current levels of consumption, demand from affluent countries can no longer be met by existing fisheries, because of over exploitation. As a symptom, the declining catches of developing countries, which are commonly too expensive for local consumption, are frequently diverted towards more affluent markets. From this, there is now a global consensus towards developing and increasing aquaculture as a sustainable source of fish to supplement and replace capture fisheries. However, the source of EPA and DHA for fish feeds has traditionally been fishmeal and fish oil, themselves derived paradoxically from marine fisheries that are equally over exploited. Carps and tilapia are the main cultured freshwater fish species in India and sub-Saharan Africa, respectively. In contrast to humans and marine fish species, where endogenous EPA and DHA production is insufficient to meet requirements, these freshwater fish species have the ability to convert a plant derived fatty acid, alpha-li-

nolenic acid (ALA), to the key omega-3, EPA and DHA. Therefore, the hypothesis we are testing in SNIPH is that feeding an ALA rich diet to these freshwater species would then translate to fish with enhanced levels of EPA and DHA. This would lead to improved nutritional quality and, consequently, health for millions of consumers, without additional pressure on the already limited fish stocks. Numerous studies have demonstrated that growing fish such as carps and tilapia on feeds based on plant derived ingredients is possible without compromising growth performance. Furthermore, there are many potential candidate crops that are rich in ALA. But these would require land, infrastructure, and vast amounts of water, involving competition for scarce resources, as they are usually already used for direct human consumption. With investment capacity limited, given the socio-economic context of farmers in developing countries, this would ultimately detract from food security. Consequently, while this is a potential solution for more affluent countries, the very nature of the materials precludes access to the people we want to help. Surprisingly, the solution may come from frequently overlooked resources. Some species of freshwater macrophytes, seaweeds, and microalgae can be rich in ALA, but do not compete with any human food resources or current animal feedstuffs. More importantly, although there is considerable intraspecific variability in composition relative to season, environment and nutrient regime, and none are a perFIGURE – TO INCLUDE fect analogue of fishmeal or oil, some of these materials


Figure 1: Some candidate species including the freshwater macrophyte species (a) Lemna Institute of Aquaculture minor, (b) Salvinia molesta and (c) Pistia stratiotes, and the macroalgae species (d) Laminaria hyperborea, (e) Ulva lactuca, and (f) Eucheuma denticulatum.

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Below: Some candidate species including the freshwater macrophyte species (a) Lemna minor, (b) Salvinia molesta and (c) Pistia stratiotes, and the macroalgae species (d) Laminaria hyperborea, (e) Ulva lactuca, and (f) Eucheuma denticulatum

08/05/2018 11:39:54

Top of the crops

The aim is improving the nutritional quality of farmed fish and, ultimately, the health of consumers

are known to be rich in protein, demonstrate very favorable amino acid profiles, and are excellent sources of vitamins and minerals. Further to this, noting that feed costs can amount to 50-60% of operational costs in aquaculture and, as these are some of the most productive plants and alga in the world and require very little management, there is potential to make major savings and improve profitability and sustainability greatly. The objective of SNIPH is to investigate the potential of locally sourced, sustainable indigenous raw materials containing significant levels of ALA/EPA/DHA as ingredients in feeds for carps and tilapia, with the aim of improving the nutritional quality of farmed fish and, ultimately, the health of consumers. While many local, indigenous materials have been investigated as potential feed ingredients for fish, essentially none of these studies has focused on the potential these may have as sources of omega-3. Preliminary screening of wild sourced candidates, based on availability and abundance in the regions of interest, identified 20 species of freshwater macrophytes, 30 species of macroalgae, one microalgae and 12 species of marine bacteria that were of potential interest. Further to this, in recognition of the potential variability, two species of freshwater macrophytes (Lemna minor and Spirodella polyrhiza) were also cultured in controlled conditions. All the candidates were then biochemically analysed to determine nutritional quality in terms of proximate composition (protein, lipid, and so on) and omega-3 content

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(ALA/EPA/DHA). The results demonstrated some suitable candidates, including the freshwater macrophytes L.emna minor, Spirodela polyrhiza and Ipomoea aquatica, particularly when cultured using optimised conditions, including fertilisers. The macroalgae (seaweed) nutritional quality was generally lower than that of the freshwater macrophytes, but Ulva lactuca, Turbinaria ornata and Eucheuma denticulatum were the best candidates from the green, brown and red phyla, respectively. What’s more, the microalga Chlorella vulgaris and at least one bacterial isolate were also very interesting. Based on the nutritional analysis, the most suitable candidates are currently being assessed in a series of fish feeding trials with rohu and tilapia. Graded amounts of each ingredient are being incorporated into nutritionally balanced, manufactured feeds in a regression design and being fed to fish for up to three months. In addition to impacts on growth performance and feed efficiency, the main objective is to determine if inclusion of these feed ingredients can enhance EPA and DHA levels in the farmed fish. We are greatly excited about the trials and look forward to reporting success in the future. The SNIPH project is led by the Institute’s Prof Douglas Tocher, supported by Dr William Clark, Will Leschen and Prof Brett Glencross, in partnership with Prof Rina Chakrabarti (University of Delhi), Prof Ramaballav Roy (University of Goa), Dr JaiGhopal Sharma (Delhi Technical University) and Prof Kumar Padmakumar (University of Kerala) in India, Dr Nazael Madalla (Sokoine University of Agriculture, Tanzania), Dr Patricia Muendo in Kenya (Machakos University, Kenya), Kenya Marine and Fisheries Research Institute, and the Aquaculture Association of Kenya in East Africa, and Dr Adam Hughes (Scottish Association for Marine Science) and Dr Cecile Brugere (Soulfish Consultancy) in the UK. For further information, please visit FIGURE – TO INCLUDE


Figure 1: Some candidate species including the freshwater macrophyte species (a) Lemna minor, (b) Salvinia molesta and (c) Pistia stratiotes, and the macroalgae species (d) Laminaria hyperborea, (e) Ulva lactuca, and (f) Eucheuma denticulatum. OTHER LOGOS – IF POSSIBLE

Figure 1: Some candidate species including the freshwater macrophyte species (a) Lemna minor, (b) Salvinia molesta and (c) Pistia stratiotes, and the macroalgae species (d) Laminaria hyperborea, (e) Ulva lactuca, and (f) Eucheuma denticulatum. OTHER LOGOS – IF POSSIBLE


08/05/2018 11:40:11

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Meeting local demand Can commercial aquaculture contribute to supporting poor people’s nutrition? By David C Little and Francis J Murray THERE has been a view in some development circles that far from aquaculture delivering on its promise to deliver a better life for the rural poor, it can actually lead to poorer outcomes. This undoubtedly reflects how aquaculture has become established in a given area and how poorer groups have gained, or lost, employment and nutritional benefits. Overtly commercial, export orientated aquaculture has attracted particular attention, even though this remains a small part of the overall picture; most aquaculture in poorer countries has grown to meet expanding local demand1. More than a decade ago, a review2 of the literature around shrimp farming and the controversy around its environmental and social outcomes concluded that there were two opposing views influencing policy. The political ecology view framed shrimp farming as being unsustainable, both ecologically and socially, and requiring major political change to protect and benefit the rural poor and protect the environment. The second view was framed as ‘better management practice’ - in brief, that the problems of the shrimp sector could be overcome through technical development and adoption of improved management. Since that time we have seen the emergence and


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consolidation of a range of international standards and certification schemes attempting to promote sustainable or responsible production, and shrimp and prawn exports continue to contribute to local and national economies. We have also witnessed huge changes in how shrimp is raised, and the methods used around the coastlines of Asia now reflect increasing variability in intensity of production3. Shrimp farming in Bangladesh, for instance, has been subject to particular criticism but recent research suggests that polarised views have often been misinformed regarding how shrimp farming impacts on the livelihood outcomes of those involved. Indeed, the Sustaining Ethical Aquaculture Trade4 project identified that coastal aquaculture was only partly about shrimp. The indigenous black tiger shrimp raised was only one part of a much more diverse harvest from these low input-output systems. The typically complex polycultures were based on both stocked and naturally recruited species and are highly dependent on salinity regime. Abdullah Mamun, a PhD student working between the Systems and Nutrition groups at the Institute, then went on to document these systems in detail and how they impacted on communities and, specifically, vulnerable individuals within them. This led him to assess the diets and nutritional status of adolescent girls within households of different types located in communities along a salinity transect – that is, from full strength seawater through intermediate saline zones to fully freshwater environments. So when an opportunity to further develop this work was offered by the IMMANA programme5, we put together a consortium that included Dr Mamun’s University in Bangladesh (Noakhali Science and Technology University), together with Dr Nanna Roos of Copenhagen, Eleanor Grieve, a health economist at Glasgow, and Drs Baukje de Roos and Alan Sneddon in Aberdeen. Additionally, we have teamed up with a well-respected international research centre based in Dhaka (icddrb). The challenge was to bridge the complexity of our emerging understanding of the nexus around the food systems, nutritional outcomes and impacts on the most Institute of Aquaculture

08/05/2018 11:42:33

Meeting local demand vulnerable to the needs of organisations supporting change in rural areas. The IMMANA programme is asking us to use data from our previous and current field work to develop a simple metric that will allow grass roots health workers to better target female adolescents most at risk from undernutrition in aquaculture communities. The project - Metric for Aquaculture Nutritional Impact for Girls (MEFANIG) - is now beginning a second round of field data collection that includes collecting blood samples of girls to assess biomarkers, and dietary assessments. A key area of inquiry is around the level of autonomy in dietary choice for adolescents and how farming systems impact on actual availability of different foods at the local level. The systems that we are working in would be familiar to those aquaculture critics of the past. People living in Bangladeshi coastal communities remain poor and vulnerable to both established and emerging threats (climate change, for example). The culture systems remain extensive, highly biodiverse and employ large numbers of people both in the value chain and on the farm. They remain almost entirely uncertified by international and even local organisations; major challenges remain in publicising and supporting uptakes of best management practices among the huge numbers of micro-producing households. One outcome is that the quality of the shrimp and crabs destined for international markets have increasingly unique but currently under-valued natural attributes. And, critically, they continue to produce large amounts of nutritionally high quality food that enters local food markets, a situation largely unreported and unrecognised in earlier accounts of coastal aquaculture in Bangladesh. Improved off-farm linkages and market connectivity have also dramatically changed opportunities to access foods for many, and led to a growing proportion of food purchased. Understanding how the most vulnerable groups can, or cannot, access such resources is critical to Bangladesh overcoming its intergenerational poverty; under-nutrition among adolescent mothers and their children remains a major concern. The MEFANIG project aims to refine the advice available to practitioners that work to improve the lives of the rural poor either through health and nutrition interventions and/or through improved food production. The lens through which we assess the impacts of aquaculture has certainly changed over the last decade but so has the urgency to communicate this more comprehensive understanding. The pressures of intensi-

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They produce large amounts of nutritionally high quality food that enters local food markets

fication of food production risk some of the nutritional benefits of farmed seafood being lost. Through working together in MEFANIG, the project team aims to contribute evidence that informs the emerging debates around nutrition sensitive aquaculture and its role in food systems that keep people healthy and support social and ecological resilience in producer communities. 1;2https://www.stir.; 3 S0044848617325292 4SEAT 2009-2014; EU- FP7Project number 222889 ; 5


Opposite page: Large amounts of Bangladeshi seafood enters local markets. Above: The IMMANA group, with Francis Murray (far left) and Dave Little (third left). Left: Dave Little and Abdullah Mamun working with communities in Bangladesh.


08/05/2018 11:42:53

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Probiotic potential Reducing smallholder dependency on antibiotics in Asia and Africa By Dr Francis Murray, Dr Mahmoud Eltholth, Robyn Shilland and Will Leschen STIRLING is leading a project aimed at improving preventative health management by smallholder shrimp, pangasius and tilapia farmers. The IMAQulate or Immunomodulators in Aquaculture project (2016-2019) is working with research and commercial partners in Bangladesh, India and Kenya. Growing local and international trade opportunities in the shrimp, pangasius and tilapia have spurred existing and new entrants to intensify production practices. There has been increasingly stringent regulation of antibiotic use in farming due to food safety and antimicrobial resistance concerns, and the lack of commercially viable vaccines in these markets. This has contributed to a booming market for probiotics, prebiotics and immunomodulators, collectively referred to as ‘prophylactic health products’ (PHPs) as alternative health management options. Although many studies have evaluated the effectiveness of PHPs, few have been independently substantiated under farm conditions. Consequently, users rely heavily on information provided by manufacturers, distributors, traders and technicians, the accuracy of which is subject to a range of potentially conflicting interests. The research is also predicated on the hypothesis that due to their more limited diagnostic and health management capacities, intensifying small-scale farmers constitute a relatively high risk group with respect to antibiotic residue detections in export markets. Probiotics are viable bacteria (for example, Bacillus and Lactobacillus spp.) that have a beneficial effect on the microbial community, either in the gut of the fish/shrimp (through feed application), or directly on the soil or water in which the animals are cultured. Prebiotics which promote growth of benign commensal bacteria may be fed alone or, more commonly, in conjunction with commercial probiotics as ‘synbiotics’. Immunomodulators contain a wide variety of substances intended to boost the animal’s natural immune system. To date, IMAQulate has inventoried more than 800 (non-vaccine) commercial aquatic PHPs routinely used by shrimp and fish farmers in the project countries to manage water quality and animal health. More than a third of these products contain probiotics (noting only a limited number of livestock probiotics are currently marketed in Kenya). Taking a value chain approach, the project has also interviewed more than 1,200 PHP retailers, hatchery operators and farmers at different production scales in order understand PHP usage trends as components of wider health management practices,


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farmer capacities and market failures surrounding their delivery and regulation of PHPs. A PHP ‘pedigree analysis’ based on indicators of use-prevalence, certification of manufacturing quality assurance, laboratory analysis of active ingredients against label claims (for close to 100 products) and expert opinion on purported modes of action was used to shortlist the most promising products for cost benefit evaluation in on-farm trials with commercial producers of shrimp (L. vannemei and P. mondon) tilapia and pangasius. In addition, a range of novel prebiotics – from extracts of mangroves to seaweeds - are being assessed for their immune modulatory properties. The greatest dependency on PHPs was observed in India’s emergent shrimp sector, spurred by widespread adoption of intensive exotic L. vannamei culture from 2009, lack of viable crustacean vaccine prophylactic alternatives and the high unit value of shrimp relative to PHP costs, compared to tilapia and pangasius. The researchers also found that due to their resource limitations and the high cost of prophylactic dosing as per manufacturer recommendation, small-scale shrimp farmers are also most likely to apply soil and water probiotics ‘therapeutically’ in response to adverse water quality cues. Their lack of diagnostic capacity makes it much more difficult for them to judge the efficacy of in-feed probiotics. Compared to larger enterprises, small-scale farmers in Andhra Pradesh with access to both ground and surface water were also found to be more likely to practice lower salinity (5-10ppt) culture as a biosecurity strategy, with implications for probiotic efficiency. Based on these findings, we have focused our first collaborative trials, with commercial partner Ananda Group in Andhra Pradesh, on evaluating shrimp production and health outcomes under probiotic, prebiotic and biofloc (as a low cost natural probiotic alternative – Plate 1) combination treatments over an extended low salinity tank nursing phase. Preliminary findings indicate significantly enhanced growth outcomes for the biofloc (BFT) and water probiotic treatments (Fig 1), which could significantly reduce grow-out time and disease exposure. The same treatments will continue to be assessed for legacy effects in a second post-treatment grow-out phase in earthen ponds (Plate 2). The findings are contributing to the design of three other trials, to be implemented with commercial producers of tiger shrimp, pangasius and tilapia in the other project countries. In Kenya, trials are being implemented by Victory

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There is a booming market for prophylactic health products as alternative health management options


Farms, cage farming tilapia on Lake Victoria (CEO, Steve Moran) in collaboration with Machakos University (Dr Patricia Muendo) and NGO SIDAI (Dr Odede Rezin). In Bangladesh, trials will be implemented by Reliant Group, a shrimp producer and the WorldFish Centre, and the pangasius trial by Bangladesh Agricultural University. The results will be used to determine low cost prophylactic options with the greatest potential for on-farm adoption by small-scale farmers and improved regulatory advice for policy makers. IMAQulate is funded by the BBSRC Newton Fund, the Department for International Development (DFiD) and the Department for Biotechnology (India).

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Above: Project collaborators, Bhimavaram, AP, India. Right: (L) Mr Kasi Viswanadha Raju (L), CEO Ananda Group and Dr Mahmoud Eltholth (R), University of Stirling examining advanced L. vannamei juveniles nursed in a biofloc tank. Ananda Group Hatchery, Kovvada, Bhimavaram, Andhra Pradesh, India. Opposite: Happa replicates in an earthen pond for the posttreatment assessment of nursed juveniles. Ananda Group R&D facility, Kovvada, Bhimavaram, AP, India.. Below: Final mean weights (with standard error bars) of L. vannamei juveniles after 32 days of extended post-larvae (PL12) nursing in covered concrete tanks under probiotic, prebiotic, biofloc (BFT) and control replicated treatments (n=5, mean temperature 29.5oC).


08/05/2018 11:45:22

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New Horizon Forging win-win collaborations between Europe and Asia EUROPEAN Union funded projects supporting the development of aquaculture in that eventually resulted in the successful bid. other parts of the world have tended to provoke a mixed reception. During this process, the realisation that aquaculture Fish farmers in Europe, for example, have often resented European taxpayers had really moved on and needed to embrace new supporting the growth of competition. approaches to stimulating innovation and beneficial Although the growth in production of Atlantic salmon has been relatively robust outcomes became apparent. The concept of using over recent decades, aquaculture in general has made very uneven progress in innovation platforms around which aquaculture stakeEurope. holders could identify challenges, vision their futures Despite significant investment and support, producers in the EU have not been and combine competencies to innovate became the able to respond to demand in the world’s single largest seafood market; there was focus of the project. a 17.8 million euro deficit in the seafood trade between the EU and the rest of the Such innovation platforms were already established world in 2015. in Europe, and it was one of these, EATIP, the EuropeBut any review of a broader range of aquaculture stakeholders in Europe would an Aquaculture Technology and Innovation Platform quickly realise the appetite for connecting with the rest of the world is an opportu- (, which led the consortium bid to build nity not to be missed. capacity in Asia to develop similar platforms. Successful are commercially driven partnerships that direct innovative Not MSPs, only istherefore, there considerable investment already in Europe based around valueresearch Multi-stakeholder platforms (MSPs) support the innoaddition tosupport Asian farmed seafood, of the largeran European aquaculture comvation with scientists, better training ofmany students entering increasingly diverse workforce, and process by facilitating knowledge sharing. They panies seemaking. significant opportunities for sale of products and services to Asia. are based on the principle that any complex challenge improve policy For example, the appetite for Scottish farmed salmon is Asia has grown rapidly in can be best resolved by different stakeholders building Partners in the project the universities of its Ghent, Wageningen and Stirling, EATIP recent years, withinclude consumers appreciating quality and provenance and, as pur-and Aqua trust and combining resources. TT, along withpower a range of Asian based Institutions, such as Nong University in Vietnam, chasing continues to grow apace in the region, thisLam could be a good model an They also acknowledge the reality that where aquaInternational Research Centre Bangladesh) commercial company (INVE, Thailand). for export led growth for(Worldfish, other farmed species inand Europe. culture has grown in importance it has done so as a Moreover, when policy makers from the EU and ASEAN discussed sectors to private sector business, rather than as a government The project is approaching the half way stage of a 36-month programme, structured around work prioritise collaboration, aquaculture ranked highly. How much this was due to subsidised or academic led activity. packages, as is the convention for EU research projects (Figure 1). previous European University partnerships with their Asian counterparts over the Successful MSPs, therefore, are commercially driven years in research and education is difficult to unpack from the fact that aquaculture partnerships that direct innovative research with is becoming such an important sector in the region. scientists, support better training of students entering Such relationships have often been nurtured through EU support in the past and an increasingly diverse workforce, and improve policy have resulted in strong alumni networks and mutual learning. making. The Horizon 2020 programme was keen to build on these foundations and to Partners in the project include the universities of bring collaboration to a new level; several meetings were held to scope out the call Ghent, Wageningen and Stirling, EATIP and Aqua TT, along with a range of Asian based Institutions, such as Nong Lam University in Vietnam, an International Research Centre (Worldfish, Bangladesh) and commercial company (INVE, Thailand). The project is approaching the half way stage of a 36-month programme, structured around work packages, as is the convention for EU research projects (Figure 1).

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[Piloting the concept Dave Little (Eurastip).indd 76

Any complex challenge can be best resolved by different stakeholders building trust and combining resources


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in Asia]

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New Horizon

Piloting the concept in Asia Three countries with quite different aquaculture profiles - Bangladesh, Thailand and Vietnam - were selected for developing MSPs. The logic is that the three national pilot programmes developed (NPPs) will form a good basis for a broader roll out of the concept post-Eurastip across ASEAN countries. This ambition led to the involvement of ASIA-FEN, a self-initiated group of fisheries educational institutions around Asia, from the concept development phase. Of course, stakeholder collaboration in Asian countries is not new to the aquaculture sector; a key step in the development of the NPPs was Stirling’s role to work with the Asian coordinating partners to map the stakeholder landscape, identifying the key players in the sector and assessing their current relationships. As expected, we found plenty of examples of collaboration, longstanding producer organisations, for example, and specific interest groups (such as processors’ and exporters’ associations). These often had important impacts, and the aim of promoting multi-stakeholder platforms is to complement these on-going initiatives and organisations with an umbrella that can support communication and targeted action throughout the sector. We have already, and not unexpectedly, identified some self-starting multiple stakeholder initiatives as part of our mapping activity. An Asian seabass farmer group in Thailand was found to have sought out specific feed products from a feed company, sourced new founder broodstock and involved a local academic to support an improved breeding programme. Our hope is that exchange in experiences, supported mobility and a range of other activities facilitated by the emergent NPP in Asia and established MSPs in Europe

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(EaTIP mirror platforms) will stimulate such processes and add future mutual benefit.

Above and left: European aquaculture

companies see significant opportunities in Asia

Towards tangible benefits Hindsight is a wonderful thing but how might MSPs have reduced the massive economic impacts of, for example, shrimp diseases that have swept through Asia? If the region had a proactive MSP in place prior to the recent acute hepatopancreatic necrosis disease (AHPND) pandemic in farmed shrimp, could we have acted to control it and mitigate its worse impacts much earlier? Could national MSPs communicating across national borders have stimulated a better regional response and more urgently designed and conducted research? These impacts are felt in both producer and consumer countries1 and solutions are likely to benefit both. Core work packages of Eurastip aim to support the development of national platforms, but the expectations is that they, in time, would lead to greater integration across the region, again building on the relationships already in place. Eurastip aims to support MSP start-up activities and partnership development between companies and academia, within the pilot MSP countries, among Asian countries and between Asia and Europe. Such activities include brokerage events, internships and company and academic exchanges. Eurastip is a H2020 project, Promoting Multi-Stakeholder Contributions to International Cooperation on Sustainable Solutions for Aquaculture Development in South-East Asia. Updates on all the opportunities are available at 1 Valderrama et al https://ir.library.oregonstate. edu/concern/conference_proceedings_or_journals/76537516q?locale=en 77

08/05/2018 11:46:59

Institute of Aquaculture

Pond performance Improving management of the Egyptian tilapia industry EGYPT is the second largest tilapia producer globally, providing affordable protein for millions of low income Egyptians based on using low cost earth pond systems. The sustainable intensification of the industry is dependent on the maintenance of fish health, but growing mortalities, believed to be related to common pathogens, are becoming a challenge. Maintaining fish health is problematic because farmers have rapidly intensified using readily available formulated diets, but on-farm power supplies are limited and most farmers rely on shared agricultural drainage water. Lab based research has shown that tilapias challenged by common pathogens are capable of improving their immune response and survival if they can select an optimal temperature regime (by expressing behavioural fever), and this could be used as a behavioural prophylaxis method. In this project, we test how modifications in pond system design and management that improve water quality and allow behavioural adaptation by fish can enhance health outcomes. This is a multi-disciplinary project conducted by two groups within the Institute of Aquaculture – the Behaviour and Welfare and the Aquaculture Systems research groups. It is funded by the Newton Caldas Fund from the British Council, with Dr David Little and Dr Simon Mackenzie as principal investigators, and Dr William Leschen, Dr Sonia Rey and Dr Mahmoud El Tholth as co-investigators. Other participants are stakeholders such as Europharma UK and WorldFish in Abassa, Cairo. The work in Egypt is done in coordination with researchers from Kafr el Sheikh University, the Egyptian union of fishermen’s cooperatives, and tilapia farmers from the Nile Delta, who participated. The research focus - pond systems design related to behavioural prophylaxis of commercial aquaculture stocks - is relatively novel and under research not just for tilapia but for a range of the main financially viable globally farmed species. The first steps were the participative research workshops performed with the farmers from the area of Kafrelsheik governorate. In these workshops, we explained the concept of behavioural prophylaxis and asked for their ideas about how ponds could be modified to achieve temperature gradients within the ponds. The farmers identified several ideas that were discussed and approved between all of us. Three different modifications were finally


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Above: Workshop between IoA staff (Prof Little, Drs Rey and Leschen) with farmers for types of pond modification.

selected (green house, dead bank and raised platforms) and a total of 45 ponds will be used for the purpose of the study. The implementation phase of the modifications is now up and running and the ponds are being monitored for water quality and temperature in different areas of the ponds (with and without modifications). Fish performance sampling every month for all the ponds over a full tilapia production cycle and management data are also being collected from each farm. Prior to the final implementation of the trial, a baseline survey was undertaken on management practices that aimed to cover the major production locations. Preliminary analysis informed the trial design, but the data is currently being analysed in full. The main outputs of this project will inform practical improvements to farmers’ pond based tilapia production and enhance the health and welfare of the cultured fish. It is hoped that current best management practices can be improved through the project and, if appropriate, it makes a contribution towards policy changes supporting sustainable intensification of Egypt’s tilapia sector.

It is hoped that current best practices can be improved through the project

Institute of Aquaculture

08/05/2018 11:48:11

Institute of Aquaculture

Pen based approach Developing diagnostic tools for tilapia lake virus By Manfred Weidmann

Some governments are not open about the degree to which their aquaculture industry is affected

THE identification of Tilapia Tilapinevirus (TiLV) in a disease outbreak in tilapia co-cultured with mullet in Israel in 2009 could have remained an isolated incident. It might not have been noted more than the reports from 1973 of Lymphocystis disease virus (LCDV), 1983 of Infectious pancreatic necrosis virus (IPNV), 1992 of Bohle virus (BIV), 2009 of Betanodavirus (RGNNV) and 2010 of Tilapia larvae encephalitis virus (TLEV), had it not been for the impact subsequent detections of TiLV had in major sub- tropical and tropical tilapia producing countries. It is noteworthy that the increased number of new virus discoveries in morbid tilapia is most likely connected to intensification of tilpaia farming in at least Israel and Thailand, but also other countries. TilV for now has been reported from the Middle East, South- and South-East Asia and South America, with Peru joining the list just a month ago. Experts discussing the issue at a WorldFish meeting in Penang in November discussed the possibility that there might be enzootic and epizootic strains of TiLV. Whereas the enzootic strains have been detected in wild tilapia in Lake Victoria in Africa for example, reports of TiLV associated disease spreading through tilapia farms in certain South-Asian countries indicates

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Above: Tilapia are cultured by a huge number of small scale subsistence farmers

epizootic activity. A confusing picture of detections and pathologies has emerged, pointing towards either more pronounced CNS or liver symptoms, or a mixture of both. It is clear that more TilV isolates and TiLV genome sequences are needed to get a better understanding of the current epizootic activity and enzootic background. As seen in other veterinary and aquaculture infectious disease outbreaks, some governments are not open about the degree to which their aquaculture industry is affected, sometimes even just short of denial. Tilapia, often termed the ‘aquatic chicken’, are cultured by a huge number of small scale subsistence farmers. Therefore, all governments openly supporting research into TilV can hope for fieldable diagnostic tools which could help to manage and control the spread of epizootic TilV into regions from where it has not yet been reported. The virology group in Stirling is currently developing rapid molecular detection assays and has already detected TilV in two countries. Currently the development of a paper based detection system, which could be used at the pen side, is planned. An international effort, spearheaded by WorldFish, is trying to raise funds for a global research framework . 79

08/05/2018 11:50:24

Institute of Aquaculture

Breeding sustainability Study of hatchery management in the Nigerian catfish industry By Suleiman Isa, William Leschen, David Little, Brendan J. McAndrew and David J. Penman

Above: From left to right, Suleiman Isa Ihiabe, Dr Penman and Alhaji Abdullahi of the Commonwealth Scholarship office at the National Biotechnology Development Agency, Abuja, Nigeria. Opposite (top): From left, two fish vendors, Dr Penman and Suleiman Isa Ihiabe on a visit to a fish smoking at Kado fish market, Abuja, Nigeria. Below: A shooter (2.7 kg) and an average sized fish hatched on the same day, from the same parents and grown under similar conditions.


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AFRICAN catfish (Clarias gariepinus) is an important aquaculture species in Africa, some parts of Asia, Europe and, more recently, Brazil. Its fast growth rate, high fecundity, tolerance and adaptation to different farming environment, have made it the choice of many fish farmers in sub-Saharan Africa. It is the second most farmed fish species in Africa (after tilapia), the most farmed fish species in Nigeria (accounting for 70% of aquaculture production) and the fastest growing aquaculture industry in many African countries. It contributes to Nigeria’s rapidly growing aquaculture industry (with an annual growth of 20% in the past two decades), the nation’s GDP (contributing about 15-20% of the 30% GDP contributed by agriculture) and the livelihoods of the many catfish farmers in Nigeria. Development of this industry has partly been as a result of increased access to husbandry and management technology. This has, over time, driven the industry from predominantly semi-intensive systems, using earthen ponds, to very intensive systems in outdoor and indoor concrete and plastic tanks, and a few recirculating systems. Despite the rapid growth and development of this industry, its main challenges are inadequate supply of good quality fish feed and good quality fish seeds (fingerlings and juveniles). The Nigerian catfish industry has, until the last four years, depended mostly on imported fish feed. This is often high quality extruded pellets, imported from the Netherlands (Coppens), Israel (Multifeed), Denmark (Aller-Aqua), Brazil (Aqualis), Ghana (Raanan), and partnerships/acquisitions involving companies such as Durante and Skretting. Being an oil producing country, Nigeria was greatly affected by the fall in global price of crude oil in the last four years, leading to a sharp reduction in the value of the naira (the local currency). Consequently, the price of imported fish feed increased without commensurate increase in the price per kilogram of fish, making aquaculture unsustainable. The few indigenous companies producing extruded pellets for catfish, also had to cope with the hike in the price of raw materials, while the on-farm feeds produced through a pelleting machine were of lesser quality (low acceptability, palatability, digestibility and water stability).

Demand for African catfish seeds (fingerlings) in Nigeria has steadily increased due to increased investment in aquaculture to meet the huge production and supply deficits of 2.0 and 1.3 million tonnes respectively - out of a total demand of 2.6 million tonnes of fish per annum. The industry relies on the relatively fast growing, imported, Dutch domesticated strain of Clarias broodstock, which were collected from locations including the Central African Republic and Cameroon in the 1970s and domesticated in the Netherlands. Until recently, most studies on the husbandry of this fish species have been based on its nutrition, physiology and production systems, with little known about the genetics and genetic management of the different strains/ populations of wild and farmed C. gariepinus within and between different countries. As a requisite for setting up a selective breeding programme to improve the overall quality of fingerlings (improve growth rate and survival; reduce inbreeding depression, cannibalism, poor quality of fingerlings and uneven growth currently reported in the industry), a survey of 321 different Clarias hatcheries and farms in Nigeria was carried out to evaluate current practices, problems and prospects. Broodstock origin, selection, management and replacement strategies, mating design, culture systems, and so on, were studied, mostly from farms in different parts of Nigeria, plus a farm and a research institution in the Netherlands and Hungary respectively. A questionnaire containing 167 questions was prepared and administered in the form of a semi-structured interview, using the traditional paper and pencil interview (PAPI) in Nigeria and computer assisted self-administration interview (CASI) in the Netherlands and Hungary. Results from the survey showed that 77% of broodstock used in the hatcheries were of farm origin, 20% from government departments and only three per cent came from wild sources (river, lakes or streams). While the majority of the farmers stated that they used C. gariepinus, only about six per cen of farmers interviewed stated that they used C. anguillaris, which is usually identified using vomerine teeth in Nigeria. This method of identification has been found to be inconsistent between different species and between different age groups of the same species, so DNA markers Institute of Aquaculture

08/05/2018 11:56:26

Breeding sustainability

are being developed to tackle this. A small proportion of hatcheries produce hybrids between C. gariepinus and Heterobranchus longifis or H. bidorsalis (known as Heteroclarias), which are advantageous in some production systems but may also raise issues of introgression if hybrids are fertile, as has been reported. More than 80% of farmers interviewed have a broodstock replacement plan. An average broodstock holding capacity was between 50 to 300 broodstock per annum; however, the survey revealed that these may come from relatively few families and that relatively few families may be produced to replace these. This practice significantly reduces the effective breeding number and genetic variation, and increases the chances of inbreeding depression. Almost half of the hatcheries obtained broodstock from grow-out farms, while a similar proportion hatched and selected their own broodstock. Most of the latter selected and used only shooters (fast growing cannibalistic fish) for broodstock replacement. This practice is based on the assumption that the shooters possess superior growth genotypes for aggression (hence, cannibalism) which could be passed on to the next generation. Very little is known about any genetic basis for the shooter phenomenon. Most of the people engaged in hatchery operations and fingerling production in Nigeria gained knowledge about this from a family member or friend, or from short courses, rather than from formal education.

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In conclusion, although the Clarias catfish industry is growing rapidly in Nigeria, some of the current hatchery practices, if these are not properly addressed, present potential threats to the sustainability of this growth. Understanding the current C. gariepinus hatchery and broodstock management practices will aid in designing effective breeding programmes and schemes aimed at improving the effective population size, reducing inbreeding depression, increasing growth and survival, thus increasing the overall quality of broodstock and fish seeds produced in the Clarias catfish industry. This PhD study research is designed to help to develop genetic management and selective breeding of Clarias catfish in Nigeria, based on the survey described above and experimental approaches to other aspects. It is funded by the Commonwealth Scholarship Commission of the UK, the National Biotechnology Development Agency, Abuja, Nigeria, and is based at the Institute of Aquaculture. For further information, contact Suleiman Isa Ihiabe ( or his supervisor Dr D. J. Penman (


Some of the current practices present potential threats to growth 81

08/05/2018 11:57:12

Institute of Aquaculture

Novel tools to treat tilapia Dual control strategies address emerging disease threat

Top right: Internal signs of francisellosis in tilapia. Middle: Vaccination of tilapia against francisellosis. Below: RPA for detection of Fno in tilapia


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FRANCISELLOSIS is an emerging bacterial disease representing a major threat to the global tilapia industry. Caused by the bacterium Francisella noatunensis subsp. orientalis (Fno), it has been recorded in 13 countries, including Europe, Asia and the Americas, where high mortality rates of up to 95% were reported. Disease outbreaks typically occur in cooler water temperatures, with severe mortalities at 23 ± 2deg C. Diseased fish show non-specific symptoms, including being off their food and lethargy, and internally there is enlargement of the kidney and spleen, with the appearance of white nodules on most of the internal organs. There are no commercial vaccines or therapeutic agents available to successfully control the disease. The bacterium is difficult to isolate (it exists inside cells) and identify, and it often goes undetected on fish farms. In addition, most of the current diagnostic assays lack sensitivity and/or specificity, are time consuming and require laboratory facilities. Fish vaccinology experts Dr Sean Monaghan, Dr Rowena Hoare and Prof Sandra Adams from the Institute of Aquaculture have teamed up with Dr Kim Thompson from the Moredun Research Institute in Edinburgh and Benchmark Animal Health to tackle this problem in a PhD project, conducted by Khalid Shahin, MVSc. Previous work by students Jose Ramirez-Paredez (PhD) and Miguel Mendoza (MSc) at the IoA had shown that it was possible to develop a vaccine, but the strategy for using this and whether it could protect fish from Fno from different geographical regions still had to be established. Therefore, Fno isolates from various locations were characterised in depth, using sophisticated proteomics techniques. These results were then used to develop and test a vaccine. Tests so far are very promising, with the vaccine inducing high survival rates of 66-82.5% in vaccinated fish compared to the control groups after experimental challenge with the Fno isolates from different geographical locations. A novel real time isothermal recombinase polymerase amplification assay (RPA) has also been developed. This molecular diagnostic test showed high specificity and sensitivity in detection of Fno; it achieved detecting limits of up to 15 molecules of Fno in less than three minutes, with a robust performance when applied to field samples in comparison to the other traditional and molecular assays commonly used in laboratory detection and identification of Fno. The study provides novel tools for controlling francisellosis in farmed tilapia. The results obtained

Tests so far are very promising, with the vaccine inducing high survival rates

lay the groundwork for improving Fno vaccine design further, and a broad spectrum vaccine that can be used globally for controlling francisellosis on farms may soon be within reach. The newly developed Fno-RPA will also facilitate the detection of Fno and it can be used as a ‘point-ofcare’ diagnostic assay in the field and in infrastructure poor settings by people with minimum training. ‘Application of an effective vaccine in association with the novel fast, cost effective, rapid and accurate RPA assay will ultimately help in controlling francisellosis in farmed tilapia,’ said Shahin. For further information, contact Khalid Shahin ( or Professor Sandra Adams ( Institute of Aquaculture

08/05/2018 11:58:16

Institute of Aquaculture

Pollution test in tropics Environmental biomonitoring tools could protect Nigerian fisheries By Isah Lawal I and Michael J Leaver THE degradation of aquatic water bodies through the discharge of toxic chemicals is increasing worldwide as global population and industrial development increase. The sustainable exploitation of fisheries, protection of animal and human health and adequate supply for irrigation and recreation can only be maintained by effective management, including methods for monitoring water quality. In many developed countries, biological effects monitoring in various forms is an integral part of effective management strategies. Tilapia are an ideal sentinel species for biological effects monitoring in freshwater tropical environments as they have a circumtropical distribution and are common, both in the wild and in aquaculture operations. They are relatively easy to capture from a variety of potentially impacted and generally under regulated water bodies throughout the tropics, and are associated with a Below: A disposal of large amount of biological and genetic knowledge. waste into a water body in It is also well established that many organisms, Kano, Kano state, Nigeria including fish, respond to pollutant insult by increasing the expression of genes, particularly those for xenobiotic metabolism. The main geographical focus for this project is Nigeria. Nigeria is endowed with a large number of freshwater and marine ecosystems.

It is the most populous black nation in Africa and the eighth largest in the world, with a population of more than 162,471,000 people. Nigeria has two distinct seasons - wet and dry although with some differences between the northern and southern parts of the country and a temperature range between 27.9- 37 deg C. Municipal sewage, industrial effluent and agrochemical use have contributed immensely to the contamination of fresh and marine water systems, causing serious deleterious effect on the biota and human health. Effective, relevant and inexpensive monitoring tools could greatly improve the management of these inputs. The aim of this project, funded by Umaru Musa Yar’adua University, Katsina State, Nigeria, was to develop a PCR based array for assessing gene expression in tilapia exposed to polluted waters. Since particular genes respond to specific pollutants it may be possible, using these types of multiple PCR assays, to determine whether pollutants are present in water bodies at biologically relevant levels, and possibly what pollutants are causing effects. In order to establish the principles of a PCR based array, we first identified, based on published literature, a suite of pollutant responsive genes in the tilapia genome. From these gene sequences we designed quantitative PCR assays that we then experimentally applied to tilapia pre-feeding larvae exposed to a range of pollutants prevalent in Nigerian water bodies. The results show clearly that different chemicals generated specific fingerprints of gene expression changes in tilapia larvae. This indicates that a standardised PCR array, such as the one described here, could be used to extend these studies to wild samples (samples from different water bodies), in order to determine whether particular contaminants are likely to be present in harmful concentrations. The development of a PCR based screening array for monitoring the biological effects of pollutants in tilapia could provide a powerful tool for the monitoring and management of water quality in the tropics, especially in Nigeria. For further information, contact Isah Lawal (isah. or Dr Michael Leaver (m.j.leaver@stir.


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The results show clearly that different chemicals generated specific fingerprints of gene expression changes



08/05/2018 11:59:29

Institute of Aquaculture and the GAA

Alliance of science Keeping it real and engaging in the global agenda By Dan Lee THE Institute of Aquaculture has a well deserved reputation for high quality applied research, much of which has been possible through its strong ties with industry. One particularly fruitful collaboration has been with the Global Aquaculture Alliance (GAA), a non-profit organisation dedicated to promoting responsible aquaculture. On multiple occasions GAA has joined forces with Stirling, both to collaborate on research projects and to help maximise knowledge transfer. In fact, indirect links go back to before the start of the GAA; the drive to create the alliance in the first place arose from fears about banned antibiotics in shrimp farming, concerns that had been highlighted in field studies by Stirling’s Janet Brown in the 1980s. In the last decade, collaboration has intensified, particularly after Dave Little joined GAA’s Standards Oversight Committee to assist in the evolution of its standards and certification programme (Best Aquaculture Practices, BAP). Little has helped to keep this committee grounded with his repeated calls of ‘don’t forget the bigger picture!’ Indeed, it is impossible to understand the full impacts and benefits of aquaculture without knowing what is going on in the wider industry, and Stirling has a particular strength at gathering the data to set records straight and help identify industry best practice. In one recent example, Stirling (Julien Stevens and Richard Newton) and GAA have helped to build recognition for the role of aquaculture by-products (heads, frames, skins and intestines) in aquafeeds and animal feeds, pointing to the importance of comprehensive lifecycle assessments when assessing overall impacts. The article, ‘It takes guts to advance sustainability in aquaculture’, was published in GAA’s online Aquaculture Advocate magazine, and Stevens used hard data to show how fish by-products are an under-valued and untapped resource. ‘With by-products representing between 25 to 50% of the weight of various fish species, we need to be looking at how the entire fish is being used,’ insisted Stevens. Well said! When considering the full impacts of aquaculture, it is also essential to consider by-crops, and again 84

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Stirling has taken the lead, for example in numerous studies in Asia. Often a multitude of small fish are harvested from ponds as a by-crop of farming a high-value, target species of fish or crustacean. These by-crops become a nutritious, cheap and locally available food resource. With this kind of information GAA, which is a global advocate for aquaculture, is able to make a stronger case for an activity that is often misrepresented as only of benefit to rich world consumers. Both Stirling and GAA are keen to improve animal welfare too and they are currently collaborating with Lyons Seafood and Seajoy on a project in Honduras. Normally, to induce rapid egg production in captive shrimp, female broodstock undergo unilateral eyestalk ablation. However, this practice is attracting attention as an animal welfare issue so Simao Zacarias, a Mossambique national, is busy developing and studying the feasibility of alternative, non-invasive strategies. Importantly, this work has quickly moved out of the lab and into a commercial setting so that the resulting procedures can be swiftly adopted by forward looking producers such as Seajoy. Meanwhile, a major new collaboration between GAA and Stirling, funded by Open Philanthropy, is now focusing on codifying best practices for tilapias and catfish. Dr Sonia Rey Planellas, the institute’s behaviourist, who has been heavily involved in salmonid welfare issues, is assessing opportunities for the transfer of lessons learnt between the species group and identifying key knowledge gaps. Researchers at Stirling, and also at Wageningen in Above: Close the Netherlands, have taken a close look at GAA’s collaboration with Stirling core activity, aquaculture certification, to assess its impact and to look out for any unintended consescientists quences. Thus far, aquaculture certification has had its greatest influence via products destined for developed world markets, where buyers often specify the need for assurance of responsible production practices. But, again with an eye to the bigger picture, this leaves vast quantities of product, particularly in Asia, that are not coming under the direct influence of certification programmes. Hence GAA has opened an office in China to make sure its certification programme is also of relevance Institute of Aquaculture

08/05/2018 12:00:49

Alliance of science

to the world’s premier aquaculture nation. This has involved working closely with leading e-commerce platforms such as and to build recognition for the BAP brand and further promote responsible production practices. Vietnam is also a major Asian aquaculture producer, where export crops of shrimp and Pangasius generate vital income for rural communities. But the success of pangasius farmers has attracted negative media coverage in the US and Europe, partly fuelled by established fishery interests that resent the competition. Keen to set records straight, in what have been dubbed ‘whitefish wars’, Stirling has played a critical role in adding balance to this debate and preventing prejudice against Vietnamese products. This kind of myth busting is typical of Stirling’s output and it also coincides with GAA’s approach. Many developing nations have a strong comparative economic advantage in aquaculture and it is in everyone’s interest to let these industries flourish rather than block them with artificial barriers. This is consistent with a ‘trade not aid’ agenda, whereby poor and emerging countries develop their own sustainable industries rather than become dependent on hand outs from rich donors. This is not to ignore that much detailed work still needs to be done to make aquaculture fully sustainable, and in this regard Stirling researchers are not scared of getting their hands dirty. Recent studies, with GAA backing, have targeted

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Stirling has played a critical role in preventing prejudice against Vietnamese products

sludge management in Pangasius ponds, trying to identify what is actually going on and how farms of different sizes respond to the requirements of certification standards. Drs Phan Thanh Lam and Francis Murray, together with MSc students Tran Thi Be Gam and Alex Pounds, carried out the study on which a report is expected very soon. GAA produces education and training materials and students have used its social welfare learning package within Stirling’s Aquaculture and Society course. This module even includes a virtual Q and A session, with leading social scientist Birgitte Krogh-Poulsen, who sits with Dave Little on GAA’s Standards Oversight Committee. In another sign of a flourishing partnership, Stirling students have flocked on to the MyGAA platform that links industry practitioners, researchers and enthusiasts. This platform hosts topical discussions and also lists job opportunities, helping to launch careers and to spread Stirling’s expertise and influence ever more widely. 85

08/05/2018 12:01:08

Institute of Aquaculture

Model farms Developing entrepreneurial tilapia aquaculture in Malawi IN 2014, the Institute of Aquaculture began a series of projects developing tilapia farming in Malawi, through Scottish government funding. The three-year Aquaculture Enterprise Malawi (AEM) project was initiated with the aim of creating financially viable, small-scale, pond based tilapia farms around Blantyre, in southern Malawi. Lessons had been learned from previous donor funded aquaculture projects in Malawi and across southern Africa which, despite significant volumes of funding, failed to have significant concrete impacts in terms of increased production and incomes generated. A consortium of relevant partners was set up, including Umodzi Consulting (an agri-business training and support organisation), Microloan Foundation (MLF), and an in-country technical team which had experience working in the commercial tilapia farming sector. Rather than an ‘aquaculture for all’ based approach in rural areas, AEM set up specific, clear selection criteria for the target individuals and sites that AEM was to support linked to peri-urban markets. It was essential that they showed entrepreneurial capacities, were numerate, market orientated, and had an appropriate fish farming site with year round water supply. AEM then carefully selected 20 individuals each year over three years, and supported them in their first year with the provision of commercially formulated feed and good quality fingerlings of Oreochromis shiranus and Tilapia rendalli. After the first 12 months, each of the fish farmers then had to pay for their own fingerlings and feed through the profits they made and Left: Willy Ntangaleya, Year 1 AEM-SHASP hatchery operator based at Makunganya village, Traditional Authority Mlumbe in Zomba Chingale.

credit provided from MLF. The AEM technical team supported the fish farmers with regular hands on monitoring and mentoring visits. These concentrated on improving their pond management, record keeping and marketing of their resultant harvests. Meanwhile, Umodzi supported the farmers in small-scale business development, with an emphasis on becoming self-sufficient and not relying on finite donor project funds. At the end of the three-year period AEM had worked with a total of 60 fish farmers, of which 47 produced clear net profits which they began to reinvest in feed for their next six-month production cycles. Towards the end of the project, five localised fish farm clusters were set up - informal groups of no more than 15 individuals, who supported each other in the transport of feed and equipment and the marketing of each other’s fish for the best prices. Based on the relative success of AEM, in 2016 the IoA secured further funding from the Scottish government small grants scheme for another three-year project, Small Scale Hatchery Aquaculture Seed Production (SHASP). Using the same selection criteria, this is now supporting and developing 15 small-scale pond based hatchery operators towards standalone financial viability. In the project’s first two years, of the ten individuals selected, eight have already demonstrated net profits through regular sales and cashflows. They are selling shiranus and rendalli fingerlings (averaging ~20,000 per year) across a radius of 150 miles from Blantyre, to both private sector grow-out fish farmers, including the AEM clusters, as well as to government fisheries departments and the National Aquaculture Centre at Domasi. Up to date activities from SHASP, as well as the previous AEM project, can be viewed on the regularly updated AEM Facebook site . There is now interest in the AEM/SHASP models from major international organisations and investors, including GiZ and WorldFish Centre, looking to scale this entrepreneurial development model up in other areas. For further details of the IOA’s activities in Malawi, contact William Leschen ( For further details on the IOA’s activities in Malawi contact William Leschen

Lessons had been learned from previous donor funded projects which failed to have much of an impact


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Institute of Aquaculture

08/05/2018 12:02:05

Institute of Aquaculture

Repair routes Predicting the impact of climate change on shellfish aquaculture SHELLFISH growth could be under threat from ocean acidification, causing changes to shell growth mechanisms and making shells more brittle and prone to fracture. Understanding these mechanisms of growth under acidification will enable predictions of vulnerable shellfish for future sustainable aquaculture. Climate change is a problem and challenge facing the shellfish aquaculture industry as CO2 levels rise causing the oceans to become more acidic. It is predicted that the pH of the oceans will fall to pH 7.7 from 8.0 by the end of the century, a big drop in pH in biological terms. Ocean acidification is a particular concern for those animals which grow shells and exoskeletons from calcium carbonate through a process known as biomineralisation. Calcium carbonate is abundant in the oceans, for shellfish such as mussels and oysters to produce protective shell structures. However, under ocean acidification the amount of carbonate available will be reduced, limiting the scope to produce protective shells. In addition to acidification caused by addition of CO2, near shore marine farm habitats are exposed to the effects of freshwater run-off and acid sulphate soils, which also decrease environmental pH. This coastal acidification is being worsened by climate change driven sea level rise and catchment driven flooding. Previous research has shown that under experiments in a lab, where we add CO2 to simulate ocean acidification and control the pH and temperature of mussel shell growth, shells had reduced growth and became more brittle and prone to fracture (Fitzer et al., 2015). In response to a reduced habitat pH caused by ocean and coastal acidification, shellfish are predicted to produce thinner shells, more prone to shell fracture through predation, harvesting and transportation to sale. This impact of ocean acidification threatens the productivity of shellfish aquaculture. In my current research project I am looking at the ability of mussels, oysters, cockles and clams to produce protective shells under future ocean acidification. Commercially available shellfish grown under laboratory simulated ocean acidification, and taken from commercial farms sites where coastal acidification already poses a threat to aquaculture, will be used to understand the process of biomineralisation. In previous work I found that mechanisms of biomineralisation can change under acidification and repair mechanisms can be employed by mussels to make amorphous calcium carbonate available for repair (Fitzer et al, 2016). This project will determine how shellfish continue to produce their calcium carbonate shells grown in acidic oceans, finding the carbonate source and route for shell production under changing acidification environments. This carbonate uptake into the shell could be mineral specific to different forms of calcium carbonate. The calcium carbonate forms of aragonite and calcite can

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Above: Field trip to Offshore Shellfish in Devon. Below: Field trip to commercial oyster farms in New South Wales, Australia.


I am looking at the ability of mussels, oysters, cockles and clams to produce protective shells under future ocean acidification


be produced by different shellfish and vary between mussels, oysters and cockles with aragonite potentially more vulnerable to acidification. This research will enable predictions of the vulnerability of aquaculture species to ocean acidification by understanding biomineralisation mechanisms between species with different minerals. And, hopefully, the research will aid the development of culture and harvesting strategies to reduce potential damage to shells during aquaculture. Farms supporting this project include Loch Fyne Oysters and Offshore Shellfish in the UK, and Graham Barclay Oysters of New South Wales, Australia, alongside the NSW Department of Primary Industries. Taylor Shellfish Farms in Washington Western US gave an account at a recent conference of problems faced by their oyster hatcheries and shellfish farms. Ocean acidification caused by upwelling of low pH waters caused malformations in larvae development and loss of oyster hatchery seed production (Barton et al., 2015). Taylor Shellfish observed impacts on shell formation in oyster larvae which was detrimental to their oyster farms. Since this acidification event Taylor Shellfish have put measures in place to sustain oyster shellfish farms under future acidification. These included hatchery water treatment to increase pH and carbonate availability for early larvae shell formation, and growing on seed in alternative locations to ensure the survival of their seed for future oyster production. The impact of this catchment source acidification will continue to be worsened by climate change, with likely effects on coastal aquaculture in many places across the globe. Management strategies such as those used by Taylor Shellfish Farms will be required to maintain the sustainable culture of these key resources. Knowledge of the expected effects of acidification on shellfish growth will aid prediction of future vulnerable species. Applying this research to mechanisms of biomineralisation in a range of commercial shellfish species will sustain future shellfish aquaculture.. For further information, contact


08/05/2018 12:03:10

Institute of Aquaculture


models Boosting oyster production in coastal lagoons of the Mediterranean THE demand for shellfish products is constantly expanding in Europe, and the Mediterranean Sea could offer potential locations for growth. After France, Italy is one of the largest consumers of oysters but the local production (50 tonnes per year) of Pacific oyster (Crassostres gigas, Thunberg, 1793) is not enough to meet the market demand, resulting in 6,500 tonnes of Pacific oysters being imported every year. The Italian region of Sardinia contributes to 60% of the national oyster production; however, a single company - Compagnia Ostricola Mediterranea in San Teodoro Lagoon - is responsible for most of this contribution. The company has therefore been selected to be a partner of the OstrInnova local government funded project, which aims to further develop sustainable oyster production in the region. Sardinia has many shallow coastal lagoons already employed for extensive farming, and it also has potentially productive sites for more intensive Pacific oyster culture, allowing this region to significantly contribute to national production. The overarching aim and practical impact of the OstrInnova project is to improve and increase Pacific oyster farming in Sardinia, providing information to stakeholders on how to best evaluate productivity in the available environments (shallow coastal lagoons); which technologies and farming methods could be used to maximise production; and how sustainable this commercial activity is. To answer some of these questions, two farming systems were compared: poches, the conventional farming system used in San Teodoro lagoon, versus Ortac units. These are a new farming tool already applied in the UK, which promise to boost flat oysters’ production by increasing survival and growth rate. The results indicate that oysters’ survival was sig- Above: Philip Graham nificantly higher (over 20% increase) in the Ortac units when compared to the survival achieved in the more traditional farming system. Nonetheless, growth and meat yield were higher

The results provide valuable information to improve the robustness of growth prediction tools


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in the poches system and of a full production cycle, 98% of the Pacific oysters farmed in the traditional system reached the smallest commercial size of 40g while only 68% of the oysters reached this size in the Ortac units. From these result, we are able to suggest a mixed use of the two different tools, the Ortac in the earlier production stages to boost spat survival in the face of challenging environmental conditions, and the poches thereafter to maximise growth potential offered by warm and rich waters characteristic of the lagoons’ environment. Finally, in order to inform sustainable development policies, oysters’ growth measured in the field and a large suite of environmental and biological parameters have been collected during two different growing seasons. These were used to validate outputs of the bioenergetics model ShellSIM ( to establish the suitability of this tool to predict Pacific oyster growth in the local context. Our results indicate that simulated growth fitted well with field observations, although seasonality and farming system used still influence the ability of this software to perform realistic prediction, providing scope for further tailoring of the model under the local conditions. These results provide valuable information to improve the pacific oyster farming and robustness of growth prediction tools in Mediterranean shallow coastal lagoons. For further information on this project, contact Philip Graham ( or Dr Stefano Carboni ( Institute of Aquaculture

08/05/2018 12:04:05

Institute of Aquaculture

Forging a female collective Project helps preserve resource for Sierra Leone oyster gatherers By Dr Francis Murray

The Njala team is led by Dr Richard Wadsworth and the IMBO team by Stirling graduate, Dr Salieu Sankoh. For further information contact Dr Francis Murray ( For more information about the Darwin Initiative visit

SINCE 2013, the Bonthe Oyster Project, funded by the Darwin Initiative, has been working with remote fisher communities living in the Sherbro river estuary marine protected area of Southern Sierra Leone. This highly inter-disciplinary project is helping to develop more environmentally sustainable, income earning opportunities for the female oyster gatherers who are most dependent on this resource. Mangroves act as a nursery for many species of finfish and shellfish, while their roots are the main substrate on which the most accessible inter-tidal oysters grow. Harvesting by root cutting and collection of mangrove fuel wood for oyster processing by a growing population is contributing to mangrove depletion. In a context of weak environmental and market regulation, economic incentives are required to help change behaviour. The project is working closely with female producers in and around the district administrative centre, Bonthe town (population 11,500), to evaluate a range of development options. These include including more fuel efficient processing methods and other post-harvest value added marketing options, such as oyster snacks and ready meals in branded packaging. The project is also facilitating an annual Bonthe Oyster Festival in support of these objectives. The second such event was due to be held in May 2018. The project exit strategy is centred on the establishment of a Bonthe Women’s Oyster Marketing Association to sustain the most promising of these activities through collective action. It is envisaged that the association will also act as a vehicle to attract and manage external income from

Plate 1: Laborious work – hand gathering mangrove oysters (Crassostrea tulipa) at low tide, Sherbro River Estuary (Francis Murray).

Plate 2: Primary processing (steaming) of oysters prior to shucking. Most production is then smoked to enable stockpiling for wholesale on weekly mainland markets (Francis Murray).

It is envisaged that the association will also act as a vehicle to attract and manage external income

Clockwise from top left: Advertising the festival; oyster gatherer; promoting more fuel efficient processing methods; working with female producers.

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the sale of carbon credits linked to prudent mangrove management. Project associate James Green, CEO of the Whitstable Oyster Company, UK (http://whitstableoystercompany. com/) has generously committed interim sponsorship to implement the Bonthe Oyster Festival over the next five years. The Darwin Oyster Project is a collaboration between the University of Stirling, the Institute of Marine Biology and Oceanography (IMBO), University of Sierra Leone ( and Njala University ( The Njala team is led by Dr Richard Wadsworth and the IMBO team by Stirling graduate, Dr Salieu Sankoh. For further information contact Dr Francis Murray ( For more information about the Darwin Initiative visit project/21013/ 89

08/05/2018 12:06:12

Institute of Aquaculture

Rearing to go Mapping bacterial communities in a mussel hatchery By McMillan S*, Desbois A, Crumlish M, Carboni S GLOBAL demand for the common or blue mussel (Mytilus edulis) continues to increase, and thus the Scottish mussel industry is expanding. Nowhere is this more evident than in Shetland which, according to the Scottish Shellfish Farm Production Survey, accounted for 74% of national production, worth an estimated £7.4 million in 2016. One barrier to increased production is the reliable availability of high quality mussel spat, the stage where the juvenile bivalves start settlement. To date, the mussel industry has been dependent on natural spatfall but abundance is highly variable and difficult to predict year-to-year. Successful hatchery rearing of blue mussel larvae to spat stage would create a reliable source of juveniles to meet industry demands. Moreover, production in this controlled way can allow for the selection of desirable traits if needed. To address this challenge, a pilot mussel hatchery based at the North Atlantic Fisheries College (NAFC) in Shetland commenced operations in the spring of 2016. In parallel with this industry backed project, a Scottish Aquaculture Innovation Centre (SAIC) and Scottish Shellfish Marketing Group (SSMG) co-funded research project called SAICHATCH is supporting the development of the hatchery through evidence based research activities. These include optimisation of mussel diets, improved metamorphosis and settlement, and providing a description of the bacterial communities within the hatchery. The Institute of Aquaculture is leading the bacteriology work package as part of the SAICHATCH consortium, which also includes colleagues from the Scottish Association for Marine Science (SAMS) in Dunstaffnage. Disease outbreaks due to bacterial pathogens are a risk in all intensified aquaculture systems but especially within a bivalve hatchery, due to inherent difficulties in employing effective prophylactic protocols. In these systems, once a disease outbreak is evident it will often be too late to intervene successfully to prevent mortalities. Monitoring of the hatchery system for changes in the normal bacterial flora present may help to predict risk periods during the delicate stages of production and identify the presence of potential pathogens prior to a disease event. Therefore, the initial aim of this work was to 90

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Once a disease outbreak is evident it will often be too late to intervene successfully to prevent mortalities

enumerate bacterial abundance within the hatchery system and then characterise the entire bacterial community including detection of any potential pathogens. To do this, mussel broodstock and larvae, algal feed and water samples were collected aseptically from various locations within the hatchery system. Then, each sample was analysed by classical microbiological and cutting edge molecular methodologies to determine the culturable and non-culturable bacterial composition. As expected for such a new system, total bacterial abundance was very low in the hatchery water. Some species of vibrio with the potential to cause disease problems were isolated from the mussel broodstock and, though these were detected only at very low levels, this is a possible route of disease transmission to larvae. As such, these results indicate the need to consider inclusion of bacteriological screening of broodstock prior to spawning as part of a biosecurity monitoring programme within the hatchery. SAICHATCH is now moving into a new stage with several further experiments, including ways to reduce overall bacterial burden such as by depuration, and the use of probiotics to provide a bacterial community that acts to out-compete potentially pathogenic bacteria. With these results and those of other stakeholders it is hoped there will soon be a fully operational commercially viable blue mussel hatchery in Scotland. For further information, contact Dr Stuart McMillan ( or Dr. Stefano Carboni (

Right: It is hoped there will soon be a fully operational commercially viable blue mussel hatchery in Scotland.

Institute of Aquaculture

08/05/2018 12:07:03

Institute of Aquaculture

Passing the stress test Insights into the use of non-ablated shrimp in commercial hatcheries By Simão Zacarias, Stefano Carboni, Andrew Davie and David C Little THIS research project aims to inform evolution of the shrimp hatchery sector towards higher welfare standards. The Pacific white shrimp (Litopenaeus vannamei), also known as Pacific whiteleg shrimp, is currently the most cultured marine shrimp worldwide. With 75% of global shrimp production in 2016, it represents an important marine food source for consumers. Rapid egg production of this shrimp is usually induced by unilateral eyestalk ablation, which involves the removal or constriction of one eyestalk through cutting, cauterising or tying to reduce the level of hormone that inhibit reproduction of shrimp in captivity. However, due to physiological imbalance and stress caused by this practice, it has attracted attention as an animal welfare issue. As a result the development of alternatives to the use of unilateral eyestalk ablation in hatcheries has become a priority for producers, retailers and seafood certifiers. The potential of using shrimp without unilateral eyestalk ablation (non-ablated) in modern egg production practices has been evaluated, and the quality of their offspring was assessed from early development stage to edible size. Our preliminary results have demonstrated that non-ablated shrimp females produce more eggs and offspring (>20% and >16%) than conventionally ablated females. Furthermore, the mortality of non-ablated females over a typical breeding period is almost half the level of ablated females. Top: Pacific white shrimp The major disadvantage of discontinuing ablation is that intact females have lower spawning intensity, Above: Simão Zacarias necessitating changes in hatchery schedules and practices. The results so far have encouraged our commercial shrimp hatchery partner (Seajoy) to move to non-ablation. The offspring produced by non-ablated females exhibited similar growth and final survival to those from ablated females, from early development stage to edible size. However, salinity stress tests

The development of alternatives to the use of unilateral eyestalk ablation has become a priority

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indicated that offspring from non-ablated females had better resilience. Buyers of shrimp from non-ablated females can be confident that they perform at least as well as post larvae and juveniles from conventional ablated broodstock. Our studies continue to bring more insights into the use of non-ablated female shrimp of Litopenaeus vannamei and the quality of their offspring. We are currently working on different feeding strategies to induce non-ablated females to maturation before they are transferred to breeding tanks. The study is also looking at the impact of those strategies on the egg and offspring production capacity of non-ablated females, quality of their offspring in terms of biochemical contents (total lipids, essential fatty acids, proteins and carbohydrates) and growth performance and survival during first development stage. Then we are going to evaluate the lifetime of non-ablated female broodstock in breeding tanks under intensive production conditions and the resistance of their offspring to other types of stress tests. After gathering all biological data, we will do an economical analysis to see how the use of non-ablated females can affect the costs and profits of shrimp hatcheries and farmers. This project was supported by the Global Aquaculture Alliance, Lyons Seafood and Seajoy. For further information, contact Simão Zacarias (simao. or Prof David C. Little ( (I would like to say a huge thank you to my beloved supervisors, Prof David C. Little, Dr Stefano Carboni and Dr Andrew Davie, for their immense support on this PhD research project.)


08/05/2018 12:08:53

[Stirling services undergo upgrade to support the sector] Institute of Aquaculture – Innovation and enterprise [‘There is a growing global need for aquaculture related expertise’]

INNOVATION and enterprise is a core pillar within the Institute of Aquaculture’s strategic plan. The institute recognises that there is a growing global need for aquaculture related expertise and so intends to expand its services to support the growing aqua-business sector.

Suitable sites for science

The institute operates four research facilities, providing the range of environmental conditions (marine, freshwater, temperate and tropical) and systems (recirculating aquaculture systems, challenge unit, constant temperature rooms, hatchery, invertebrate) required for animal experimentation and state-of-the-art analytical laboratories.

Stirling services undergo upgrade to support the sector

The sites are:

INNOVATION and enterprise is a core pillar within Stirling Analytical Platforms: Stirling the Institute of Aquaculture’s strategic plan. The recognises that there is a growing global  institute Stirling Experimental Aquatic need for aquaculture related expertise and so inFacilities: tends to expandStirling its services to support the growing aqua-business sector.  The Niall Bromage Research Institute operatesFreshwater four research facilities, providing the range of environmental conditions Unit (NBFRU): Buckieburn, Denny (marine, freshwater, temperate and tropical) and (recirculating aquaculture systems, chal systems Marine Environmental Research lenge unit, constant temperature rooms, hatchery, Laboratory (MERL): invertebrate) required for animalMachrihanish, experimentation andCampbeltown state-of-the-art analytical laboratories. The sites are: • Stirling Analytical Platforms: Stirling Currently, the Experimental university isAquatic investing in the • Stirling Facilities: Stirling installation of a modern day recirculating • Niall Bromage Freshwater Research Unit aquaculture system hatchery and smolt unit (NBFRU): Buckieburn, Denny at the Niall Bromage Freshwater Research Unit (NBFRU) at some Buckieburn. • Marine Environmental Research Laboratory placement of of the infrastructure with the (MERL): Machrihanish, Campbeltown purchase of new equipment and installation of a Currently, the University is investing in the of eighteen 600L primarily tanks. Thesefor tanks have autoDue toinstallation be operational by autumn 2018, this unitsetwill be utilised research and education of a modern day recirculating aquamatic feeding, waste feed collection and environpurposes in system line with the and institute’s culture hatchery smolt unitstrategic at the Niallplan. mental monitoring and are intended primarily for Bromage Freshwater Research Unit (NBFRU) at fish growth performance studies. Buckieburn. Significant work has also been research done to identify The facility will also be made available to industry for bespoke contract services relating to Due to be operational by autumn 2018, this unit future needs for infrastructure and research supfreshwater production. will be finfish utilised primarily for research and education port at Machrihanish as part of the wider Institute purposes in line with the Institute’s strategic plan. review. The facility will also be made being availablemade to industry TheaUniversity is currently working with Additional investment is also to install new aquatic laboratory forkey pathogen challenge for bespoke contract research services relating to partners to identify future development opportuniwork within thefinfish existing on-campus facilities, with aspiration that thisof facility willand be ready to use freshwater production. ties the that meet the future needs the industry Above: The MERL facility Additional investment is also being made to education sectors. at the start of 2019. at Machrihanish install a new aquatic laboratory for pathogen chalThe University of Stirling is dedicated to suplenge work within the existing on-campus facilities, porting the Institute, not only to ensure that it The institute’s Marinethat Environment at Machrihanish, plays a dual role with the aspiration this facility will Research be ready to Laboratory continues to (MERL) be a renowned international centre use at the start of 2019. for world classsecondly, research andto teaching, but a to contract research firstly, to support academic research and teaching and, provide The Institute’s Marine Environment Research Lab- expand the opportunities for business academic serviceoratory which supports the development of new and innovative products by partners in industry. (MERL) at Machrihanish, plays a dual role integration, providing a catalyst for innovation and - firstly, to support academic research and teaching enterprise, and a hub for the creation of sustained and, secondly,provides to provide large a contract research serpartnerships. The laboratory scale facilities for experimental studies on fish in seawater. It also vice which supports the development of new and The are now working on hosts innovative a range products of research resources, including liveUniversity culturesandofInstitute commercially important pathogens by partners in industry. an exciting capital development plan that aligns such asThe sealaboratory lice andprovides pathogenic amoeba. large scale facilities for with the Institute’s strategic plan 2017-2021. experimental studies on fish in seawater. It also Contact Alistair McPhee, head of NBFRU (a.m.mhosts a range of research resources, including live, for information about the Niall cultures of commercially important pathogens such Bromage Freshwater Research Unit and James Dick as sea lice and pathogenic amoeba. ( for all other facilities. MERL continues to operate as a good laboratory practice (GLP) compliant facility, successfully completing the biennial GLP inspection by the Medicines and Healthcare Products Regulatory Agency (MHRA). Further progress has been made with the re-


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There is a growing global need for aquaculture related expertise

Institute of Aquaculture

08/05/2018 12:09:44

Institute of Aquaculture - Nutrition Analytical Service

Centre of excellence Providing customers around the world with first class analysis • Oil/fat content of feeds fish and raw materials • Carotenoid and xanthophyll pigments • Fatty acid analysis by gas chromatography • Omega-3 status of blood and tissue samples • Acid, peroxide and anisidine values of oils and feeds • Lipid class analysis • TBARS

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and is trition

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THE Nutrition Analytical Service (NAS) was created in 1998 and is internationally recognised as a centre of excellence for nutrition o focus on alsspecific , andwith basisresearch, ineacids. utfatty d roand a regular anlipids acid are equipped ood fatty The Institute Aquaculture’s laboratories ciallyof bl pe es cal samples, with HPLC, LCMSMS, GC, GCMS and GCMSMS capabilities, as well as modern sample preparation facilities. The current customer base boasts more than 43 organas Canada, isations across oducerinsNorway, t princluding pigmtheenglobe, noidDenmark, rganic caroteChile, Peru, Israel, Switzerland l the Czech Oiand us from the American Chemist statRepublic. The NAS provides its 20 core customers with reports on ysis. a regular and routine basis, and also provides a service for the analysis of human and animal clinical samples, ments set ireanalysis. especially acid requ the fatty with blood t em consisten The NAS continues tod from n two of the libratio g an havecaapproval testin oforganic carotenoid pigment producers as a centre competencemain n edita cralso m Acand excellence analysis has tio Approved Chemist d Kingfordo ite n from the Unof status from the American OilsChemist as (AOCS) for suchSociety mparison atoryOilco Fatty Acid Profile analysis. e inter-laborMarine The service is compliant with the quality management system consistent with the requirements set out in ISO/ IEC 17025:2005 ‘General requirements for the competence of testing and calibration laboratories’, and is working towards achieving accreditation from the United analysis Service (UKAS). This includes classAccreditation id  Lip Kingdom participation in appropriate inter-laboratory comparisons S as formal proficiency testing schemes or ring trials.  TBAR such The E offers the following analytical measurements: taminNAS

 Vi ureomega-3 analysis Blood  Moist NAS conducts analysis of omega-3 fatty acids for a  Protein  Facilities - 2.indd 93

• Vitamin E • Moisture • Protein • Ash • Dioxins • PCBs • PBDE’s

range of pharmaceutical companies, health professionals and pathology laboratories. NAS also supports research projects that involve the measurement of omega-3 status. Since 2007, NAS has worked with research and commercial partners to conduct analysis of fatty acids in human red blood cells (RBC). A rapid method is also provided for measuring omega-3 status using a single drop of whole blood. The blood sample is obtained via a finger prick collection kit and is immobilised on pre-treated card prior to analysis. The measurement of long chain omega-3 fatty acids is of particular interest due to their widely acknowledged benefits for human health. Other analytical services In addition to NAS, the institute boasts a number of additional services through its Stirling Analytical Platforms. It works across the aquaculture sector providing total health management for fish stocks, providing expert diagnosis of fish diseases and can provide regular fish health screening using parasitology, bacteriology, histology, virology and specific pathogen certification. Live and freshly dead samples of fish can also be brought directly to the team for examination. With world leading experts in breeding and genetic improvement, the institute can provide support for commercial broodstock management and on-growing practices for established and new fish species. This includes characterisation of reproductive development, guidance and implementation of optimal biotech approaches to maturation control, light set-up and efficiency, population sexing and maturation (sex steroid profiling, ultrasound scanning), smoltification regimes and monitoring (ATPase activity). As the only facility in the UK to have a range of sea lice strains, including drug naïve strains, the insitute has developed an in-depth understanding of the sea lice life cycle, allowing scientists to investigate and identify how to combat this serious production and welfare issue. Water quality testing continues to be a service that the institute provides to a wide variety of business, not just within the aquaculture sector, providing advice on water collection protocols, through to sampling regimes and processing. Its laboratory can undertake all statutory marine and fresh water analyses to European standards, and many non-standard techniques which are of value to statutory bodies, water companies, aquaculture companies and aquaculturists. Supporting aquaculture skills development The institute also provides a range of training opportunities for continued professional development. This covers, but is not limited to: • Fish Health: o Basics in sampling o Disease identification o Treatment and management of fish diseases

• Aquatic Animal Nutrition and Food Safety • Environmental Management

Contact technical manager James Dick ( for more information about the Nutrition Analytical Service. For further information on any services or training opportunities contact 93

08/05/2018 12:11:33

Institute of Aquaculture

Learning culture Stirling courses, from first degrees to continuing professional development WE are delighted to announce our new short training course in Fish Health and Welfare – a two-day programme designed to provide participants of all backgrounds with a solid understanding of the biological particularities of fish, fish health and disease, disease prevention, fish welfare and relevant legislation. You can expect a hands-on approach to fish dissection and tissue sampling techniques, as well as interactive group based discussion of case studies. Additionally, our programme delivers an overview of salmon production in Scotland. Access to the core course does not require previous experience in aquaculture. Quite the reverse, the core course is designed as an entry point to learning the key concepts of commercial aquaculture. If your work is associated in any way with the aquaculture supply chain, this training is tailored for you. The first edition of the course in Fish Health and Welfare is planned for the end of June/early July and will be run in our facilities on the University of Stirling campus. Accommodation and catering are included in the package and there will be good opportunities for networking. Places are limited. If you are interested, please contact Alex Pargana, one of our vets, who is coordinating this short CPD (

questions such as: what determines the distribution of individual organisms and populations? Why are some ocean provinces more productive than others? What impact does human activity have on the health of the oceans? Why are some fisheries sustainable and others not?

The Institute of Aquaculture also delivers a range of two-week continuing professional development training in key areas relevant to aquaculture business and regulatory services. These extended CPD programmes are based on the topics from our Master courses and are taught at Scottish Credit and Qualifications Framework (SCQF) Level 11. Our teaching is rooted in our cross-disciplinary, internationally recognised expertise. You can consult our portfolio and find out more about the CPD content on our website: And please do contact us if you would like us to design a bespoke training course according to your specific needs and interests:

Postgraduate courses MSc Sustainable Aquaculture Learn the principles of aquaculture and what drives the viability of aquatic production systems, including socio-economics, environment, nutrition, reproduction, genetics and disease. Advanced topics include broodstock management; feed formulation; health control; environmental management and modelling; engineering; policy and planning; livelihoods; economics and business studies; and ecotoxicology. Exploring these topics will give you the

Postgraduate research courses MPhil and PhD Students on our MPhil and PhD programmes in Aquaculture and Aquatic Veterinary Studies can focus on any areas within the varied suite of activities undertaken by the institute. You can review our staff pages to find a potential supervisor or check our website for upcoming research opportunities.

Learning opportunities Studying at the University of Stirling means experiencing the best that Scotland has to offer. We provide an inspiring, engaging and collaborative student experience. Combined with lifelong career management and employability skills, we are committed to ensuring you realise your potential, and are equipped with the knowledge and expertise needed to succeed in your field of study. As a university, Stirling is first in Scotland and third in the UK for graduate employability, with 98% of students in work or further study within six months of graduating. We offer the following undergraduate and postgraduate courses: BSc (Hons) Aquaculture This innovative course will train you in all subjects appropriate to global aquaculture. Aquaculture—or aquatic agriculture—is much more than ‘fish farming’ and includes culture of species such as prawns, shrimps, mussels, oysters, crocodiles, turtles and algae. Aquaculture already produces more than half of all of the fish consumed globally. BSc (Hons) Marine Biology This course is truly multi-disciplinary. It draws on other biology disciplines, such as ecology and the physical and environmental sciences, to answer 94

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Institute of Aquaculture

08/05/2018 12:12:23

Learning culture

Mastering aquaculture Postgraduate courses for professional careers

skills in development, entrepreneurship and decision making to forward a career in aquaculture production, supplies, services, regulation or other sectors. MSc Aquatic Pathobiology This course will help students gain an understanding of the biology, husbandry and environment of farmed aquatic species, in addition to specialist expertise in the prevention, diagnosis and treatment of aquatic animal diseases in cultured organisms. MSc Aquatic Veterinary Studies This course is specifically aimed at students with a veterinary science qualification to train them in the wide range of disciplines and skills necessary for the investigation, prevention, and control of aquatic animal diseases. Students will gain an understanding of the biology, husbandry and environment of farmed aquatic species, in addition to specialist expertise in aquatic animal diseases. MSc Aquatic Food Security Learn the global issues affecting seafood production and trading—from farm to fork— and the role they play in achieving global food security. This course covers key factors affecting aquatic food production, post-harvest protocols, post-mortem metabolic events and the microbial/chemical processes key for food safety and quality. Distance learning and short courses The Institute of Aquaculture recognises the importance of flexible learning environments. MSc programmes can already be taken on a discontinuous basis and we will be developing alternative delivery routes for degree courses. Modular online distance learning options will be made available for those unable to relocate or those who wish to expand their expertise through continued professional development options.

We provide an inspiring, engaging and collaborative student experience

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THE Institute of Aquaculture’s MSc programmes enjoy a high international reputation, with graduates active in the aquaculture industry all around the world. Current MSc programmes director John Bostock said: ‘We teach 35 to 50 MSc students per year across out portfolio of MSc courses. Students come from a wide range of academic and career backgrounds, from fresh graduates in biology to business entrepreneurs or vets with prior professional experience. ‘It is also a very international environment, with around one third of the students from the UK, one third from other European countries and one third from the rest of the world. This usually includes Africa, Asia, North and South America and sometimes Australia or New Zealand.’ Director of teaching and learning Mike Leaver explained the approach to postgraduate teaching: ‘All the teaching is in modules, with all students starting with a common core of essential topics and then selecting from a range of more specialised modules, which can lead to the different degree outcomes that we offer. ‘These include: Sustainable Aquaculture, Aquaculture and the Environment, Aquaculture Business Management, Aquaculture and Development, Aquatic Food Security, Aquatic Pathobiology, and for people with existing veterinary qualifications, Aquatic Veterinary Studies. ‘This provides flexibility for the students to focus on the areas that are of most interest to them. It is also a very intensive programme, taking just one year. The last third is spent on an individual research project, which is often carried out with external partners, sometimes overseas or involving work at a fish farm.’ Bostock said: ‘Aquaculture is a very applied subject. We aim to ensure all students understand the basics of different species and systems and how they interact with the wider environmental, social and economic contexts in which they have developed.’ When asked how the institute specifically addresses the issues of graduate employability, he replied: ‘We use a lot of group work to encourage teamwork and leadership skills. We also build communication skills through assignments that require different approaches, such as oral presentations and discussions, written reports or the production of posters, web pages or videos. ‘We also organise visits to commercial aquaculture producers, feed and equipment suppliers, processors and other research establishments to help students understand different roles within aquaculture.’ Recent MSc graduate Julien Stevens, now with Kampachi Farms in Hawaii, said: ‘The most challenging aspect of the course for me was working non-stop, one project after another, week after week; it gets challenging at certain points, but by the end of it I feel I have got a lot out of it.’ Ben Weis, now with Scottish Sea Farms, agreed, saying: ‘Everything is manageable, but you get your skills in time management and how to organise yourself – which is definitely worth it!’ And Alexandra Pounds, now working with OSO Farming, an organic shrimp producer, in Madagascar, summed up her year in Stirling as simply, ‘a better experience than I could possibly have imagined’.


08/05/2018 12:16:33

Supply chain – AKVA group Scotland

Adding value to aquaculture Growth and innovation support a major Scottish success story

THE Scottish aquaculture sector has a proud and impressive track record, becoming the UK’s number one food export in just a few decades, and helping to underpin the reputation for excellence in the country’s food and drink industry. Not only does aquaculture generate significant economic wealth, but it does so in some of the most remote and rural communities in Scotland, providing career opportunities for the next generation. While the producers are the sector’s ‘brand ambassadors’, they are supported by a significant supply chain, which responds with creativity and innovation to the challenges and needs of the sector. A recent study (2017) sponsored by Highlands and Island Enterprise - the Value of Aquaculture to Scotland - clearly articulates the value of the sector to Scotland and the role that the entire value chain brings to Scotland, with more than 12,000 FTEs (full-time equivalents) and value in excess of £620 million. AKVA group Scotland (AGS) is one of several companies supporting the sector, positioning itself as a provider of high quality, innovative products, backed up by a best in class service. The company supplies and supports a wide range of equipment, from land based systems, through the seawater phase, to the farm gate, helping producers to farm sustainably and efficiently. The product range includes containment and farming technology to help keep stocks secure and improve feeding efficiency, while reducing benthic and environ96

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mental impact. Headquartered in Inverness, AKVA group Scotland employs around 80 people, including highly skilled technicians, engineers and electricians. With satellite offices in Lochgilphead, Stornoway and Kishorn, the group can provide a fast and responsive service to its customers. Technological innovation is key to the development of the industry and, as a general maxim, 50 per cent of the total value creation in the aquaculture industry stems from producer related activities. The remaining value creation comes from direct and indirect services to these core industries, including technology and service providers. By combining both innovation and the ability to create products locally, AKVA group Scotland seeks to establish the maximum value, along with the most efficient solutions for the industry. Through its global network, it is then able to deliver its Scottish products into the international aquaculture marketplace. Technological innovation and the development of direct and indirect services is crucial in understanding the total value creation from the aquaculture industry. It has been estimated that for every job created in primary production or farming, there are five more created throughout the supply chain and this is often forgotten – leading to an underestimation of the value creation in the total aquaculture industry cluster. Examples of current innovation projects being developed by AKVA group Scotland include the Polar Lift System (PLS-500), new camera and imaging technology, environmental sensing packages to support water quality decision making, lighting systems and net cleaning pump systems. Specifically, the PLS-500 has been developed to help farmers operate safely and rapidly in more exposed, higher energy locations, where heavier duty equipment is required, and automation is a necessity. The new FNC8 ROV net cleaning system means net cleaning is much quicker and more efficient, with none of the drawbacks and issues associated with net damage from existing systems. In support of the FNC8 ROV, AKVA group Scotland has also developed a pump system which provides the power and water pressure which underpins the perforInstitute of Aquaculture

08/05/2018 12:17:28

Adding value to aquaculture

Clockwise from top right: AKVA technicians develop solutions specifically tailored to meet producers’ demands.

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For every job created in farming, there are five more created throughout the supply chain

mance of the FNC8 system and provides the client with an integrated and proven solution. AKVA group Scotland also provides technical support and development expertise for the group’s export division, which covers the Mediterranean, Middle East, Far East, India and Africa. This has not only opened up new product development opportunities but has also created a strong Scottish export potential. By looking at all the needs of the global aquaculture market, AKVA group Scotland can develop equipment here in Scotland to meet the different environmental, economic and cultural conditions in these developing markets, while also bringing new technology to the home market. And as part of a global group, the company benefits from inward investment, as well as the spin-offs from wider research projects being carried out in Norway and further abroad. These projects are focused on farming in more remote and exposed locations and include submersible pens and feed systems, remote control systems, net handling systems and innovation in barge design. Hybrid power barges have been designed to significantly reduce the power consumption and operating

noise levels, thus providing a benefit to both staff and the environment. Other benefits include lower CO2 emissions and reduced operating costs, with less fuel and service, providing the producer with both savings and green credentials. In addition to the direct impact on the economy of these fragile areas, there are also considerable contributions to the social fabric and community in which the sector operates. Like most companies involved in the aquaculture sector, AKVA group Scotland supports local community initiatives, with sponsorship of many activities throughout the Highlands and islands, including shinty in Lochcarron, school football in Uist, and Simmer Dim in Shetland. By developing technology focused on solving the biological challenges of the aquaculture industry, AKVA group Scotland contributes to the continued development of a sustainable industry with fish welfare as the most important success factor. AKVA group Scotland is proud to be a part of this incredibly successful industry, which strives to farm sustainably, as well as to help and sustain communities in remote areas on Scotland’s furthest compass points. 97

08/05/2018 12:17:49

Institute of Aquaculture

Farewell to Professor Brendan McAndrew Stirling pioneer retires after acclaimed international career BRENDAN McAndrew retired on May 4, 2018, after 39 years’ service. The Institute of Aquaculture would like to express all its gratitude for his impressive contribution, from the early days of the institute. His outstanding and sustained research, collaborations and innovation over the years, in the area of fish genetics, have inspired thousands of graduates all over the world and attracted many researchers to the University of Stirling. His work has contributed to the development and expansion of the world aquaculture sector. An important achievement has been the establishment of the tilapia reference collection from wild specimen, collected in Africa back in the 80s. These fish have provided the basis for a significant body of research, and have been distributed to other labs and commercial operations all over the world over the years. His roles as the Genetics and Reproduction research group leader, director for research of the Faculty of Natural Sciences at the University of Stirling, president and treasurer of the International Association of Genetics in Aquaculture, editor of proceedings in ‘Aquaculture’, adjunct professor at BodØ University College, and PI in many large collaborative projects, have contributed very significantly to the worldwide reputation of the Institute of Aquaculture as the leader in aquaculture research and training. With an h index of 43, more than 100 peer reviewed publications - including studies on 34 different fish species across the world, Brendan can be proud of his achievements. The institute staff wishes all the best to Brendan for his retirement, which will involve, for sure, lots of fishing … tight lines!


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Above: Brendan McAndrew. Top: With Dave Penman (second left) and former students Marine Herlin, Anu FrankLawale, Alex Hilsdorf, Cameron Brown and Jose Mota-Velasc

Brendan can be proud of his achievements

Institute of Aquaculture

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Institute of Aquaculture

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Institute of Aquaculture Special May 2018  

Institute of Aquaculture, University of Stirling

Institute of Aquaculture Special May 2018  

Institute of Aquaculture, University of Stirling