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EASTBIO: The microbial black box of soil – Does what’s inside matter?

College of Medicine and Veterinary Medicine

About the Project

The soil microbiome encompasses a huge taxonomic diversity with a single gram of soil containing as many as 52,000 individual species. This microbiome mediates a number of key soil functions including N cycling processes which are both important for maintaining soil fertility and implicated in the production of the greenhouse gas N2O. This makes understanding the relationship between the soil microbiome and soil function important to developing sustainable soil management strategies. Most N cycling process are carried out by a phylogenetically diverse group of microorganisms which show a high level of functional redundancy. This has led to the suggestion that microbial community composition and associated diversity are less important in determining rates of N cycling than associated soil physiochemical conditions. However microbial controls on soil function remain poorly understand and are often masked by physiochemical parameters. Plants are known to select for unique soil communities within soils associated with their roots (the rhizosphere) creating a system which can be manipulated to allow testing of the relative roles of community selection and soil conditions on rates of N cycling. The aim of this project is therefore to determine the relative roles of microbial community composition (as altered by the presence of different plant species) and environmental factors on the rates and products of soil N cycling. Additionally we will look to identify under what conditions microbial communities may exert a control on N cycling by looking at both neutrally and deterministically selected soil communities.

This project will characterise soil communities and N cycling rates in a long term grass trial run at the James Hutton Institute in Dundee where a variety of grass species known to promote differing levels of N2O production from soils are grown in both monoculture and mixes. We will use a range of cutting edge next generation sequencing and bioinformatics approaches to characterise the soil microbiome while also taking detailed soil functional measures. N cycling rates will be determined using a range of 15N stable isotope labelling methods which allows the quantification of N2O and N2 produced by denitrification. Multivariate statistics will be used to partition the relative effects of the microbial community and environmental factors on N cycling. Controlled environment experiments will be used to determine whether plant driven community selection by a range of grasses and grass mixes is deterministically or neutrally controlled and the implications on the rates and products of N cycling.

Funding information and application procedures:
This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (DTP) .

EASTBIO Application and Reference Forms can be downloaded via

Please send your completed EASTBIO Application Form along with a copy of your academic transcripts to

You should also ensure that two references have been send to by the deadline using the EASTBIO Reference Form.

Funding Notes

This opportunity is open to UK and international students and provides funding covering stipend and UK level tuition fees. The University of Edinburgh covers the difference between home and international fees meaning that the EASTBIO DTP offers fully-funded studentships to all appointees. There is a cap on the number of international students the DTP recruits. It is important that we know from the outset which fees status category applicants fall under when applying to our university.

Please refer to UKRI (View Website ing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/) and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria (View Website).

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