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,
Stirling
FK9 4LA

Email: c.j.payne1@stir.ac.uk

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.

Contact:
School of Ocean Sciences
Bangor University
Menai Bridge
Anglesey
LL59 5AB
UK
Email: gmonkman@mistymountains.biz

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

Publication
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.

Contact

Biosciences
College of Life & Environmental Sciences
University of Exeter
Exeter
EX4 4QD
UK

Email: ll292@exeter.ac.uk