Phd Student Vacancy

3 weeks ago


Dundee, United Kingdom The James Hutton Institute Full time

**Background**: This project provides an exciting opportunity to use computational biology to explore the diversity and interactions within agricultural soil microbiomes. Soil is an environment with one of the highest levels of diversity and abundance of microorganisms on earth, and these microbes collectively form the soil microbiome. Future food security for the planet depends upon developing sustainable agricultural practices and this includes methods to maintain a “healthy soil” microbiome.

Currently, soil microbiome research has focussed on bacteria and to a lesser extent fungi. But soil also contains viruses, protists, phage and eukaryotes. Future soil microbiome research needs to focus on the integration of data from not only the bacteriome and mycobiome, but also the virome, protistome, phageome and eukaryome. This is the aim of this PhD project.

**Aims**: To use the UK-CMCB metagenomic datasets to analyse the total complement of microorganisms in rhizosphere soils from a crop grass and a crop legume.

Objective 1: Identify the bacterial, fungal, viral, protist and eukaryotic composition of rhizosphere soils from wheat and fava bean.

Objective 2: Map the multi-kingdom microbiome components to potential functions and cluster them into functional guilds.

**Methods/Training**: This project is 100% computer based and will involve using both established and novel workflows for data analysis and modelling. This project will provide training in computational biology, software and data carpentry, and microbiome analysis and modelling (relevant to both the fields of agriculture, plant pathology and medicine). The computational biology training will include shell script writing, writing software code (in the R programming language), the use of the Linux operating system, GitHub and the use of SLURM to submit jobs to Hutton’s high-performance compute (HPC) cluster. A PhD student who has these computational and modelling skills will be equipped to gain employment in an array of diverse settings, including academia and industry.

The James Hutton Institute is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.

The James Hutton Institute is a: Stonewall Diversity Champion; Athena SWAN Bronze Status Holder; Disability Confident Committed Employer and a Living Wage Employer.

The James Hutton Institute is Happy to Talk Flexible Working.



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