PhD Studentship: Using the structure and function of oyster and hatchery microbiome to inform active microbe management and mitigate production failures

University of Exeter - College of Life and Environmental Science

Main supervisor: Dr Tim Bean (CEFAS), Prof Angus Buckling (University of Exeter)

Bivalve hatcheries produce millions of juvenile animals for on-growing in aquaculture farms worldwide. This process uses controlled systems to assist bivalves through the most vulnerable stage of their lifecycle, the free swimming larval veliger. Hatcheries are fundamental to the Commercial success of the UK oyster industry. However, within the hatchery environment it is not uncommon for larval batches to suffer large scale mortalities. Entire groups of animals can be lost to facultative pathogens, in a little understood and unpredictable manner. It is well understood that the microbiome status of an organism inherently affects the ability of that individual to deal with insult by opportunistic pathogens. Furthermore, modification of the microbiome, through probiotic treatment, can increase larval survival under certain circumstances. This project aims to build on previous research demonstrating the beneficial effect of probiotics on this stage of hatchery culture by characterising the bivalve and hatchery microbiome and consequently attempting to understand and then manipulate the microbiome to a beneficial state.

On completion of initial sampling (and throughout ongoing opportunistic sampling) the project will utilise facilities at Cefas and Exeter to condition oysters, spawn and grow the larvae through the first two weeks of their life, whilst experimentally manipulating the microbiome. The experimental regime will begin with an initial characterisation of the lab microbiome, followed by several forms of hypothesis driven manipulation of the system. Manipulation will be achieved by antibiotics, bacteriophage, addition of microbes discovered and cultured in earlier stages, addition of facultative pathogens to observe changes in microbiome and manipulation of the nutrient environment. If successful, the methods used in hypothesis driven experimental work will be taken into field situations and tested in the hatchery environment. To undertake these analyses, over the three years, the student will build heavily on their current knowledge of microbiology, molecular biology, bioinformatics and phylogenetics and will be trained in bivalve culture in laboratory and hatchery environments.

For the full project description and how to apply please click the 'apply' link below.

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South West England