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Soil microbiome transplantation. PhD in Biosciences (SWBio DTP)

  • Full or part time
  • Application Deadline
    Monday, December 02, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Prof Angus Buckling, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors
- Dr Bram Kuijper, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
- Professor Samuel Sheppard, Milner Centre of Evolution, University of Bath
- Prof James Chong, Department of Biology, University of York
- Dr Rob Griffiths, CEH
- Dr Mike Salter, AB Agri

Location: University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE

Programme Overview
The South West Biosciences Doctoral Training Partnership (SWBio DTP) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research. This partnership also includes the following collaborative partners; Marine Biological Association (MBA), Plymouth Marine Laboratory (PML), Swansea University, UCB Pharma, University of the West of England (UWE) and SETsquared Bristol.

These institutions represent a distinctive group of bioscience research staff and students, with established international, national and regional networks, and widely recognised research excellence. As research leaders, we have a strong track record in advancing knowledge through high-quality research and teaching, in partnership with industry and the government.

For more information about the programme structure, please visit

Funding for 2020/21
These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description

The rapid reduction in soil health is one of the most pressing issues facing food security, and novel solutions are urgently required. A key determinant of soil health is the soil microbiome, which can be negatively affected by intensive agricultural practices. Re-establishing “normal” soil microbiomes by transplantation is likely to play a key role in promoting soil health, because of the positive feedback between biotic and aspects of the soil environment.

The idea of microbiome soil transplantation is not new, but has often proved ineffective because of a failure for the healthy invading microbiome to invade and dominate the resident community. We have recently successfully achieved successful microbiome transplantation in the context of biogas production (Sierocinski et al. 2017, Current Biology) by invading from rare mixtures of multiple communities. Communities act as semi-coherent units, with the community most efficient at using resources dominating. This greater resource-use efficiency resulted in higher levels of biogas being produced.

In this project, we will first apply this approach to improving soil health in experimental soil microcosms. Our preliminary work suggest the approach will work, because more efficient resource use means more rapid nutrient cycling and improved soil health. We will refine the approach to identify what makes a successful, invading community, to avoid the need of “blindly’ mixing multiple soil communities together. Specifically, we will: 1) determine how long term co-evolution within microbiomes is likely to affect resource-use efficiency; and 2) prior adaptation to fluctuating versus constant environmental conditions affects the ability of a community to invade a new environment.

These novel questions will be addressed using a combination of theory (supervised by Bram Kuijper, a bio-mathematicians who has worked extensively on the evolution of biotic interactions) and model soil microbiomes that we have developed. These 5 species microbiomes have been stably coexisting in nutrient media the lab for more than 6 months, uniquely making long term evolution experiments feasible.

The simplicity of the system makes them amenable for determing underlying mechanisms through genomic analyses (under the supervision of co-supervisor Sam Sheppard, at Bath) and metabolomic analyses (in collaboration with Prof James Chong, York).

To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria in line with UKRI guidelines. See the following webpage for further details

A fully-funded four year SWBio DTP studentship will cover

• a stipend* at the standard UKRI rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard UKRI rate)
• additional funds to support fieldwork, conferences and a 3-month internship

Funding Notes

SWBio DTP funded studentship available for September 2020 entry. The studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20, on a full time basis.

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