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

Project Description:

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.

The student leading this project will take environmental and animal samples from UK oyster hatcheries several times during year one. Samples will be processed through Illumina 16S and metagenomics sequencing pipelines, and also through bacterial culture protocols. Samples will be assessed to characterise A) the variability of the microbiome, B) the presence of obligate and facultative pathogens within each sample, C) The presence and relative quantities of microorganisms of potentially therapeutic interests and D) the functional consequences of different microbial taxa, through bioinformatic “reverse ecology” and direct measurement of microbial interactions in vitro. In addition, the student will opportunistically sample at hatcheries when there are mortality events in to understand the alterations to the microbiome that occur during these events.

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.

The supervisory team for this project includes:

Dr Tim Bean of Cefas has several years’ experience working with Bivalve molluscs, including rearing, spawning, conditioning of oysters in conjunction with disease challenge development. In addition, Dr Bean runs the next generation sequencing systems for Cefas and has over 10 years of practical molecular biology experience. Tim has co-supervised several PhD students and acted as primary supervisor for PhD and Masters students.

Professor Angus Buckling of Exeter University (Penryn campus) is microbial evolutionary ecologist, with a particular focus on the consequence of microbial interactions for disease and ecosystem function. He has well-funded group and has supervised >10 PhD students, most of whom have continued in successful academic careers.


For further information and how to apply please visit http://www.exeter.ac.uk/studying/funding/award/?id=2520