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NERC E4 Networks of influence: how soil microbial communities respond to land use

   School of Biological Sciences

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  Prof Thorunn Helgason, Dr Joe Taylor  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Interested individuals must follow the "how to apply" link on the Geosciences E4 Doctoral Training Partnership web page: http://www.ed.ac.uk/e4-dtp/how-to-apply


The link between soil microbial community structure and function and land use will be investigated to inform soil management for sustainability

Project background

Soils are one of our most threatened ecosystems, and it is an urgent priority to understand how to manage and conserve them, while maintaining ecosystem services such as carbon storage, nutrient provisioning and agricultural productivity

From 2015 to 2020, Prof Helgason’s group were involved with two Soil Security Programme consortium grants, SoilBioHedge and MycoRhizaSoil. These farm-scale experiments studied the response of crop genotypes, arbuscular mycorrhizal inoculation, and soil microbial and earthworm communities to ley/fallow and minimum tillage conservation agriculture interventions. These field scale, designed experiments with replication are fully archived and have significant metadata associated with them, held by collaborators at the Universities of Leeds, York and Sheffield. 

Dr Taylor is Senior Scientist within the Molecular Ecology group in the Soils and Land Use science area at the UK Centre for Ecology and Hydrology, and is working with UKCEH archive data to understand how land use affects eukaryotic microbial community composition.

You will have access to data from all these projects, and to the soil and plant samples archived from the Soil Security Programme projects. In the first instance, you will use existing data to carry out network analysis of the interactions between bacteria, fungi and other eukaryotes (algae, protists, animals), analysing both taxonomic composition and function. This will enable you to identify potential relationships such as parasitism or mutualism. You will generate hypotheses to test the link the between different interactions within the microbiome and land use, and develop group specific molecular techniques to analyse them, using the archive and field samples. Finally you will work with the UKCEH soil archive to use the UK wide data and model soil microbiomes at the UK landscape scale.

This is a unique opportunity to apply cutting edge molecular and data analyses to a pressing issue in ecosystem conservation.

Research questions

  1. What are the relationships between taxonomic and functional composition of microbes in soils undergoing different land use (hedgerow, pasture, arable (conventional and minimum tillage)?
  2. What are the key taxa and/or functional groups that respond to change in land use?
  3. Can targeted molecular methods be designed to track these taxonomic groups or functional genes?
  4. Do microbiomes and microbial function track land use at the landscape scale?


The project will combine bioinformatic and community ecology analysis methods with molecular ecology, and DNA profiling of soils.

Year 1: Use existing data from MycoRhizaSoil and SoilBioHedge projects to create taxonomic and functional data across a variety of taxonomic groups (Bacterial, general Eukaryotes, Fungi). Generate co-occurrence networks among different groups, and use analysis to generate hypotheses around microbial communities and land use types, eg Hedgerow, pasture, arable (conventional and minimum tillage)

Year 2: Design experiments to test hypotheses. This will be done first with the sample archive, using novel molecular ecology approaches, eg analysis of particular functional genes or taxonomic groups using high throughput sequencing or qPCR. Second, a field sampling campaign at appropriate sites could be carried out. 

Year 3. Hypotheses around microbiome function and land use will be tested using the CEH countryside survey data for soils, which includes microbial biodiversity and other metadata across the landscape scale. 


A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills.


We are seeking a student with an interest in microbial ecology, soils, sustainability and land use. 

You will have a degree in ecology, microbiology or environmental sciences, with some experience of labwork, preferably with DNA handling, and of computational analysis using R or Python.


The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity

The “Institution Website” button on this page takes you to our Online Application checklist. Please complete each step and download the checklist which provides a list of funding options and guide to the application process.

Funding Notes

This project is eligible for the E4 Doctoral Training Partnership. The E4 projects are currently available for full NERC studentship funding which is competitive by interview to UK, EU and International applicants (The fee difference will be covered by the University of Edinburgh for successful international applicants.).
For application details see http://www.ed.ac.uk/e4-dtp/how-to-apply
Further details here - https://www.ed.ac.uk/e4-dtp/how-to-apply/e4-dtp-projects



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