Dr X Harrison
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the Great Western Four alliance of the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus five Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad training in earth and environmental sciences, designed to train tomorrow’s leaders in earth and environmental science. For further details about the programme please see http://nercgw4plus.ac.uk/
Project details
Emerging infectious diseases pose a significant threat to wildlife health. Understanding the factors that predict individual susceptibility to infection is vital for developing practical strategies for wildlife conservation and disease control.
Bacterial communities living in association with hosts, known as the microbiome, can be key to protecting individuals from infection by pathogens. In the UK, populations of common frog (Rana temporaria) differ markedly in their response to the pathogen ranavirus. Whilst some populations have exhibited catastrophic outbreaks of the disease ranavirosis, others appear relatively stable, and these patterns appear to be linked to variation in their skin microbiome. However, almost nothing is known about what determines variation in amphibian host microbiome structure. Colonisation of host-protective bacteria is strongly influenced by the environment, and one possibility is that the presence of environmental contaminants such as antimicrobial pollutants can negatively affect these colonisation dynamics, with important consequences for host health.
Project Aims and Methods
This project will use a combination of field surveys, controlled experiments and molecular tools to investigate the links between the amphibian skin microbiome, ranavirus infection, and antimicrobial pollutants in populations of the UK common frog. The overall aim of the project is to test the hypothesis that antimicrobial pollutants alter the susceptibility of amphibian hosts to disease by modifying structure of their skin microbiome.
The student will:
- perform an extensive survey of wild common frogs in a network of sites in the south west of England to estimate spatial (co)variation in skin microbiome structure, using both 16S amplicon sequencing and shotgun metagenomics.
- use qPCR to quantify ranavirus infection loads in the environment, and how these infection loads change seasonally
- generate chemical profiles of pondwater from each site to quantify spatial (co)variation in levels of antimicrobial compounds
- use inhibition assays to test the ability of the common frog mucosome to inactivate ranavirus virions in vitro
- use controlled experiments on frogs reared in common garden conditions to test the effect of exposure to pond water containing varying levels of pollutants on skin microbiome structure
We will ensure from the very outset that the student is given every opportunity to influence the PhD research direction. Although we have established a well defined science proposal the various elements can be tailored also to the developing interests of the student.
Training
This multidisciplinary project will equip the student with a broad suite of skills, including:
i) fundamental scientific skills in experimental design, numeracy, and communication.
ii) field skills involving capture, handling and sampling of wild amphibians throughout a network of sites in the UK
iii) molecular genetics skills, including bioinformatics and use of genome data bases, to quantify the amphibian skin microbiome through 16S typing and shotgun metagenomics.
iv) analytical chemistry techniques to quantify the profile of antimicrobial compounds and their metabolic transformation products in the environment using LC-MS.
v) statistical and spatial analysis to integrate data from field sampling, ecotoxicology and molecular datasets
Funding Notes
NERC GW4+ funded studentship available for September 2019 entry. For eligible students, the studentship will provide funding of fees and a stipend which is currently £14,777 per annum for 2018-19.
Eligibility;
Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award but no stipend. Applicants who are classed as International for tuition fee purposes are not eligible for funding.
References
-Harrison XA, Price SJ, Hopkins K, Leung WT, Sergeant C, Garner T. Host microbiome richness predicts resistance to disturbance by pathogenic infection in a vertebrate host. bioRxiv. 2017 Jan 1:158428.
-Price SJ, Garner TW, Nichols RA, Balloux F, Ayres C, de Alba AM, Bosch J. Collapse of amphibian communities due to an introduced Ranavirus. Current Biology. 2014 Nov 3;24(21):2586-91.
-Bates KA, Clare FC, O’Hanlon S, Bosch J, Brookes L, Hopkins K, McLaughlin EJ, Daniel O, Garner TW, Fisher MC, Harrison XA. Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure. Nature communications. 2018 Feb 15;9(1):693.
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