PhD Studentships: Can the gut microbiome support fish health? Chris Payne

Chris Payne

Stirling University (supervisors: Mags Crumlish and Simon Mackenzie) 2016-19

Can the gut microbiome support fish health?

The intestinal environment of vertebrate animals is colonised by a complex microbial community, termed the microbiome. In fish, this community is extremely diverse and made up of more than one trillion bacteria/g of intestinal contents. Recent meta-analysis has revealed that many fish species share a core gut microbiome community comprised of five key bacterial phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. Furthermore, members within this core microbiome are thought to have been selected throughout evolution to play vital roles in promoting and maintaining their host’s physiology and health status.

My PhD focuses on how this microbial community can support fish health through microbially-mediated gut functions. To investigate this, I am using next generation sequencing of the bacterial 16S rRNA gene, to profile the microbiome communities in different farmed fish species and explore how certain husbandry practices can influence these communities and their mediated functions within the fish host. In particular, my research will i) explore how antibiotic compounds influence the microbiome communities in different farmed fish and ii) investigate how manipulated microbiome communities impact on gut health in the fish host as measured by changes in immunity, metabolism and gut function.

Overall this project aims to improve our understanding of the core microbiome community composition in different fish species and help support the development of novel husbandry methods to improve the resilience of farmed fish. Data obtained from this project will be essential to the global aquaculture industry on multiple platforms – more critically addressing current attempts to reduce or find alternatives to antibiotic use in fish farming.

For further information please contact:
Institute of Aquaculture,
University of Stirling,


PhD Studentships: “Population Genomics and Molecular Evolution in Salmonids” Kevin Schneider

Kevin Schneider

University of Glasgow (supervisors: Kathryn Elmer and Colin Adams) 2016-19

Thesis Title: “Population Genomics and Molecular Evolution in Salmonids”

Some groups of salmonids, such as charr and whitefish, repeatedly and rapidly diversified into co-occurring ecomorphs in various lake habitats. This diversification potential has, at least to some degree, a genetic basis. Using transcriptome data from various species of salmonids, I am screening for footprints of natural selection to identify the genetic toolbox that could enable some salmonids to diversify rapidly.
Various populations of Arctic charr, which is often considered the most variable vertebrate on earth, are characterised by ongoing or recent diversification into mostly benthic and limnetic ecomorphs. To learn more about this evolution-in-progress, I am using whole-genome data to understand how adaptation to different environments shapes the genomes of diverging ecomorphs. Importantly, I am also focussing on the amount of ongoing or past gene flow between ecomorphs and among populations and its potential effects on the divergence process.
It has been shown that the demographic history of populations can influence the degree and nature of diversification. However, we know little about the interplay of demography and adaptation or selection at the genome level. With the help of in-silico simulations of large genomic elements and comparisons of the obtained genomic signatures of selection under various demographic scenarios to real-world data, I am trying to disentangle the complexities of these evolutionary processes to inform analyses of empirical data.

PhD Studentships: Social behaviour of the Archer fish (Toxotes spp.) Nick Jones

Nick Jones

University of St Andrews (supervisors: Luke Rendell and Mike Webster) 2015-2018

My PhD focuses on the social behaviour of Archer fish (Toxotes spp.) and their learning. Renowned for their ability to shoot down terrestrial prey by ‘shooting’ jets of water at them archer fish may be capable of using social information from conspecifics to learn to perform specific behaviours. I am investigating this and exploring the various factors that affect their learning and social dynamics. I am supervised by Luke Rendell and Mike Webster at the University of St Andrews in collaboration with Stefan Schuster at the University of Bayreuth.

PhD Studentships: Transgenerational effects of chronic maternal stress experience in sticklebacks Agnieszka Magierecka

Agnieszka Magierecka

University of Glasgow (supervisors: Neil Metcalfe and Kath Sloman) 2015-2018

The effects of environmental stressors on organisms have been extensively studied in a wide range of phyla, including mammals, birds and fish. It has also been shown that environmental stress experienced by mothers may affect the phenotype and behaviour of their future offspring. The questions that remain largely unanswered are whether chronic exposure of mothers to environmental stressors can cause such effects in offspring and how these are influenced by the timing and duration of stress. Untangling the relationships between these factors would give an insight into the effect that environmental changes (and the potential for increased environmental stress) may have on wild fish populations. My project aims to address these questions using an established laboratory population of three-spined sticklebacks (Gasterosteus aculeatus). Only the male three-spined stickleback provides parental care, and so the non-genetic influence of the mother on the offspring is limited to the substances deposited in her eggs or ovarian fluid at the time of egg production and spawning. This provides an opportunity to use an experimental approach to study whether environmental stressors acting upon females in the period leading up to spawning affect the growth, survival and behavioural phenotype of their offspring. This project addresses the question of transgenerational effects of chronic mild environmental stressors using a chronic, unpredictable stress protocol and non-invasive and minimally stressful method of measuring water-borne cortisol.

PhD Studentships: Integration of Sea Angling Associated Catch and Mortality for Stock Assessment

Graham Monkman

University of Bangor & CEFAS

There are c. 1 million recreational sea anglers (RSA) in the UK, spending annually over £1.2 billion and their removals of marine fish can be quantitatively comparable to commercial landings, as revealed by landings of the European sea bass, Dicentrarchus labrax. Hence angling removals should be included in stock assessments and fisheries management, accounting for catch and release and post-release mortality rates.

RSA catch has only been included in stock assessments of Baltic cod; a gap recognised by the European Commission, and in the Common Fisheries Policy that requires members to report on catches by RSA for some species to give a clearer picture of how fishing affects stocks. RSA data on commercially significant species are also required at a local level under the Marine and Coastal Access Act to provide an evidence-base when balancing the needs of marine environment users. However, national RSA assessments are expensive and complex, especially in the UK where sea angling is unlicensed, so there is little evidence to inform the development of a policy for UK sea angling despite the sector’s importance.

My research will seek to scope, develop and validate transferable, innovative techniques in the capture of RSA data on marine fish species of recreational and commercial importance, primarily within ICES ecoregions E and F. This work will comprise three synergistic strands:

To engage with the UK RSA community to determine the extent of existing catch data recorded by anglers and to collate those data to construct time series of catches and compare against existing fisheries independent and dependant time series.

To develop, evaluate and pilot practical, reusable low cost technological solutions to complement RSA data recording, including natural language processing of social media sources; machine vision in species identification, and optical character recognition in form processing complemented with SMS, email and mobile solutions and their application to local and national angler survey programmes.

To evaluate the viability and define success criteria for a citizen science programme on the ongoing assessment of recreational sea angling, based on the outcomes of the preceding strands.

School of Ocean Sciences
Bangor University
Menai Bridge
LL59 5AB

PhD Studentships: Differential Susceptibility to Copper in Wild Populations of Three-Spined Stickback (GASTEROSTEUS ACULEATUS)

Lauren Laing

University of Exeter

Supervisor(s): Eduarda Santos & Rod Wilson

Most aquatic environments in the UK and worldwide have been affected by anthropogenic environmental stressors. Such stressors vary from chemical pollution to habitat fragmentation and to changes in abiotic parameters such as temperature and dissolved oxygen or carbon dioxide. Populations of fish inhabiting these environments are often exposed to combinations of stressors and, as a result, their sustainability is critically dependent on their ability to adapt to the local environment. Despite this, legislation to protect the environment from chemical contamination is often based on toxicological measurements conducted under optimal laboratory conditions and that does not take into account the variation in susceptibility of wild populations or the multiple stressors affecting these populations.

For metals, extreme cases exist of fish populations that can survive in highly contaminated waters, including a brown trout population in the River Hayle, where concentrations of metals far exceed the LC50 for this species. Furthermore, even for populations of fish inhabiting relatively un- impacted waters, their toxicological responses to metals can vary significantly. This highlights the need to understand natural and exposure-induced variations in the response of fish to pollutants, in order to appropriately manage and protect fish populations in their natural environment.

My research explores three key questions, firstly to determine if wild populations of three spined sticklebacks exhibit differential susceptibility to copper and if those characteristics can be inherited under control conditions. Secondly, my research aims to determine if differential susceptibility can be induced by exposure to copper during early life. Thirdly, I plan to investigate the fitness cost associated with differential susceptibility to copper in this species.

Together, this research will allow for a greater understanding of the variation in the responses to chemical stressors in wild populations, how they are induced and maintained and what are the consequences of changes in susceptibility to a pollutant on other parameters of fundamental importance to population sustainability. The data will build on previous data generated at Exeter, and will have implications for toxicity testing and regulation and for the management of wild fish populations.

My report on my attendance at the Canadian Conference for Fisheries Research is here

Uren Webster, T. M., Laing, L. V., Florance, H. & Santos, E. M. 2014. Effects of glyphosate and its formulation, Roundup, on reproduction in zebrafish (Danio rerio). Environmental Science & Technology 48, 1271-1279.


College of Life & Environmental Sciences
University of Exeter


PhD Studentships: Fish Ecology of Mesophotic Coral Reef Ecosystems

Dominic Andradi-Brown

University of Oxford

Supervisor(s): Alex Rogers (Oxford) and Dan Exton (Operation Wallacea)

Mesophotic coral reef ecosystems (MCE) occur in tropical regions extending from 30 m to the limit of the photic zone, c. 150 m. These reefs are often connected to shallow coral reef ecosystems, where it is suggested they provide an important reservoir of recruits for coral and fish populations. Existing reef fish studies are highly depth biased mostly < 30 m, making the importance of mesophotic reefs to overall reef resilience in the face of human disturbances such as overfishing largely unknown, with a lack of evidence for whether fish populations on shallow reefs and adjacent MCEs are connected. This study addresses this important information gap by using advanced diving technologies coupled with a newly developed stereo-video system and molecular ecology techniques to better understand fish communities by examining fish biomass distributions and community structure down depth gradients from shallow reefs to MCEs and by exploring the connectivity of MCE fish populations down depth gradients with shallow reefs and between mesophotic reefs. This project is being conducted in partnership with Operation Wallacea with fieldwork principally based at their field site on Utila, Honduras where MCEs connected to shallow reefs have been identified but are unstudied. The aims of the project are twofold, first to Investigate biomass and community structure. Fisheries value and ecological service provision requires biomass to be quantified as it provides a better indication of functional pressure exerted by a fish-feeding guild than richness or abundance. Fish biomass along transects will be assessed by stereo-video surveys capturing the shallow reef to MCE gradient at various fished and protected sites. Biomass will be standardised using fish length-weight relationships, through data from local fisheries monitoring programmes to obtain local length to weight ratios, but for any fish species not caught locally, through available datasets (e.g. Fishbase). To allow patterns in fish biomass and community structure to be explained, benthic composition will be quantified using point intercept video transects, quantifying coral (genera and morphology), algal and other coverage. Physical parameters will also be recorded including temperature, light and turbidity and HOBO loggers for detailed year-round temperature and light readings. The second aim is to Investigate connectivity in MCE fish populations. Levels of population connectivity between populations of depth-generalist fish species with residents found on both shallow reefs and MCEs are not known. This has major implications for conservation and sustainable management of MCE fisheries, as well as the design and location of marine protected area networks. Many studies have demonstrated the ability of molecular techniques such as microsatellites to identify population structure; these protocols can be applied to assess connectivity down depth gradients and between MCE specialist species on small spatial scales. Non-lethal fin clippings will be collected from fish using a hand net and a clove oil anaesthetic mix. Care will be taken to return individuals to the reef where they were caught. To assess connectivity along depth gradients, samples of depth-generalist reef associated fish will be collected at different depths at several sites. To assess population connectivity between MCEs, an MCE specialist fish species will be identified samples collected at several sites. Contact: Ocean Research and Conservation Group Department of Zoology University of Oxford The Tinbergen Building South Parks Road Oxford OX1 3PS UK Email: Twitter: @dandradibrown URL:

PhD Studentships: Assessing and predicting the impacts of non-native fish parasites: From Hosts to Ecosystems

Josie Pegg

Bournemouth University

Supervisor(s): Robert Britton and Demetra Andreou

The global introduction rate of freshwater fish has doubled in the last thirty years, primarily through fish movements in the aquaculture industry. When fish are moved from their natural range and introduced into a new range, they are likely to be host to a number of parasites. Whilst some of these parasites might be lost during the introduction process, often some will remain. If transmitted to native species, infection consequences can include pathological damage and, potentially, modifications to host behaviour, fitness and energetics. Given that native parasites have recently been shown to play important roles in food webs through, for example, increasing connectivity, nestedness and robustness, then further introductions of parasites into ‘infectious food webs’ have potential to modify these food web properties.

My research explores this using three non-native fish parasites introduced into UK freshwaters in order to identify their consequences for individual hosts, assess how these scale up into population and community effects, and determine their modifications to the structure of the invaded food web. Three non-native parasites will be studied which represent groups with varying complexity in their lifecycles so that they can demonstrate how, for example, the number of hosts in the life cycle affects food web structure.

Ergasilus briani has a simple life cycle, involving host-to-host transmission in their preferred host species of roach Rutilus rutilus and common bream Abramis brama. Bothriocephalus acheilognathi has a complex life cycle involving intermediate hosts before their definitive fish host becomes infected, where the final host here is common carp Cyprinus carpio. Anguillicoides crassus also has a complex life cycle but it involves several paratenic hosts (in which the parasite remains immature) before being transmitted to its preferred definitive host, in UK waters the European eel Anguilla anguilla. Transmission to eels is often through predation of a paratenic host.

Using both field case studies and experimental mesocosms the consequences of these parasites for food web structure will be assessed using two principal methods: food web topology and stable isotope analysis.

My report on my attendance at the Canadian Conference For Fisheries Research 2014 is here.


Faculty of Science and Technology
Bournemouth University
Talbot Campus
PooleBH12 5BB

PhD Studentships: The effects of Different Beta-Glucans on fish microflora: Immunomodulation and disease protection

Sarah Harris

Keele University

Supervisor(s): Dave Hoole, Mark Skidmore and Dieter Steinhagen

There is ever increasing pressure on fish populations to meet the demands placed on them both as a food source and an economic commodity. Aquaculture plays a significant role in reducing the need to rely on wild populations, thus helping species that have been pushed dangerously close to extinction to start recovering and, additionally, lessening the strain on wild cohorts of more stable species. As with any farmed population keeping large numbers together can drastically increase the spread of pathogenic disease which may result in high mortality rates and economic losses.

Since the immune protection induced by vaccination tends to be specific to the target pathogen and there is a movement away from more traditional methods of coping with disease outbreaks, such as antibiotic treatments, there is an increased interest in the concept of improving overall health by increasing general immunity. Immunomodulants act by enhancing the general immune defence which can result in a higher rate of survival during infection. Immunomodulative compounds, such as β-glucans, are already widely used within the farming industry and are known to have a positive impact on fish health although the mechanisms behind their actions are still mostly unknown. Additionally, commercial products undergo several stages of processing before reaching the target organism therefore the physical structure of the final immunomodulative components have yet to be fully elucidated.

One of the simplest, least stressful means of exposing fish to β-glucans is to incorporate the compound into the fish feed. Upon consumption, the β-glucans come into contact with the commensal microflora population within the gut. There is an important symbiotic relationship between a host fish and its commensal bacterial population which, if disturbed, may have both positive and negative effects on gut functions and general health. In addition to having immunomodulatory properties upon the host fish, β-glucans can also be utilised as a food source by certain bacterial species. The aim of my research is therefore to establish how immunomodulants affect both the immune response of the host and the ecology of the microflora of the intestine. Whilst there are many publications related to either the host or the microflora as separate entities, there is very little on bridging the gap between the two within ichthyology. Using the common carp (Cyprinus carpio) as a model host and a range of known β-glucan structures, in vitro studies will determine the effects of β-glucans on individual bacterial species and in vivo trials will establish effects on the resident microflora population and the innate immune responses in the gut of the host fish.

Another mode of exposing fish to β-glucans is to add them as a bathing agent. This has been shown to have positive health benefits including increasing the rate of wound healing in carp, but the effect this has on the environmental microflora has not yet been studied. In order to establish the extent the inclusion of known β-glucan structures are able to alter waterborne microflora populations, molecular microbiological methods will be employed to analyse closed circulation systems both with and without the presence of the selected host fish.

This project is a development of the work undertaken under the auspices of the EU ITN “Nemo” which established the effect of MacroGard®, a commercially available β-1,3/1,6-glucan, on the immune status and health of common carp.


School of Life Sciences
Keele University

LinkedIn: Sarah Harris

PhD Studentships: Reef Structural Complexity and the Dwindling Habitat for Diverse Caribbean Fish Communities

Charlie Dryden

Newcastle University

Supervisor(s): Nick Polunin & Steve Newman

Scleractinian corals are ‘ecosystem engineers’, providing most of the foundations of the coral reef ecosystem, specifically creating a three-dimensional physical habitat and micro-climatic conditions for a plethora of species and ecosystem services. Corals act as a refuge from predators, provide habitat surfaces for prey and offer nesting sites for brooding species. Threats to the existence of coral reefs such as climate-related bleaching, diseases, nutrient susceptibility and fishing-related impacts, have created an urgent need to more fully understand the role corals, and the habitat they create, play in supporting the diverse and abundant coral reef communities.

Early work on coral reef degradation focussed largely on phase shifts from coral to algal dominated states and effects on community structure. This rather ignored the role of the physical structure of the reef sustained by corals. Structural complexity has been correlated with higher levels of diversity in both terrestrial and marine habitats, including coral reefs. However, these findings relied upon simplistic habitat measures and broad community metrics. It is necessary for this relationship to be examined in greater detail to identify which aspects of structural complexity are important to specific components of the community. Related to this, there is scarcely anything known about how mobile species interact with the reef framework. Yet the utilisation of space on reefs by fish is key to predicting how degradation will affect the ecosystem and the humans that rely on them. Such understanding will offer insight into how species, trophic groups and size classes react to loss of habitat structure.

The Caribbean has been undergoing continued losses of structurally complex Acropora spp. and Montastraea spp. of coral since the late 1970s. Stress-tolerant corals that form smaller and less complex colonies, such as Porites spp. and Agaricia spp. have now become relatively more abundant and the consequences of this shift are scarcely known. While the coral cover of Caribbean reefs has been declining for 40 years, changes in fish community structure were negligible until 10 years ago. These changes in the Caribbean fish communities are thus unlikely to be exclusively linked to live coral-cover loss. Unlike their Indo-Pacific counterparts, no Caribbean reef fish are obligately dependent on living corals for food or refuge, therefore decline in reef fish communities appears to more closely relate to generic effects of the loss of reef structure.

Temporal trends in Caribbean reef complexity and community structure have been explored through sparse existing data however, there is at present no methodologically-constrained information on spatial trends in Caribbean regional complexity, yet this is crucial for understanding the current status of reefs, the extent of ongoing changes, and the implications for environmental managers.

This study will examine the concept of structural complexity in natural systems and detail the spatial patterns of reef complexity across 10 Caribbean countries. It will then focus on the relationship between complexity and the fish community and the behavioural interactions between fish and the reef structure.

Marine Science and Technology
Newcastle University NE1 7RU