How can microbiomes and soil biodiversity support food security?

Underground soil biodiversity and ecosystem services

Photo by Dylan de Jonge on Unsplash

This project will investigate how underground soil biodiversity is affected by novel horticultural practices.

The studentship starts in October 2020 and is funded by NERC. 

Apply for this course

Read the eligibility criteria and application guidance below, then send your application to

Application deadline: 6 January 2020

Project background

Human impacts on the natural environment are now so great that we are eroding our own economies and food security.

Studies of how land-use change affects the biota nearly all consider only above-ground biodiversity, and most focus on taxa not strongly linked to key ecosystem services. Not enough is known about impacts on underground soil biodiversity, carbon and nutrient cycling.

The soil microbiome (bacteria, fungi and other protists) and small invertebrates are a major component of soils, are essential for maintaining key terrestrial ecosystems, and interact with the roots of plants in ways that affect plant growth, health, and resistance to pathogens.

Project Aims and Methods

Recent studies on horticultural crops such as tomato, strawberries and apples have shown that adding certain bacteria and fungi to crops can make it easier for plants to use the surrounding biodiversity by stimulating soil microbiota and endophytes (prebiotics), and to improve plant nutrition or protection against pathogens (probiotics), and subsequently may allow a reduction of the use of fertilisers and pesticides.

However, little is still known about the effect of novel horticultural practices on underground soil biodiversity and how to predict the response to crop types under conventional and organic management.

Statistical modelling to date mainly uses species data obtained by morphological identification but the integration of DNA-based taxa data from high throughput sequencing would also allow to consider bacteria and microbial eukaryote taxa data in addition to soil invertebrates in policy-relevant models.

The overall aims of the project are

  • to assess and compare the biodiversity of microbiome and invertebrate communities from horticultural soils and crops using environmental DNA sequencing and metabarcoding and the range of biodiversity measures that these make available
  • to integrate DNA sequencing data into policy-relevant models of how soil community composition will respond to novel horticultural approaches and management practices
  • to evaluate if biotic responses are consistent among major taxa, guilds and habitats; and 4) refine existing models of how soil communities respond to agricultural management

The PhD student will be able to develop their own specific questions to address as part of the studentship, and have the opportunity to gain expertise in analyzing soil microbial and invertebrate assemblages through a combination of environmental DNA and high-throughput sequencing, bioinformatics, statistical, meta-analytical analysis techniques. The studentship will be part of the H2020-funded Excalibur project that aims to evaluate the multifunctional potential of belowground biodiversity in horticultural farming. The newly-generated data will be supplemented with data from published papers, which will augment the PREDICTS database.


  • Molecular and microbiology techniques: DNA extraction methodologies from environmental samples, PCR, high throughput sequencing technologies.
  • Bioinformatic analysis: techniques for metabarcoding and microbial community structure analyses.
  • Statistical modelling: Estimation of a range of biodiversity metrics; mixed-effects modelling of how local (alpha) diversity and spatial and temporal turnover (beta diversity) respond to land management practices.
  • Science communication skills: The PhD student will have opportunities to training in communication skills and participate at NHM public engagement events.


To be eligible for a full award a student must have:

  • British Citizenship or; 
  • Settled status in the UK, meaning they have no restrictions on how long they can stay,
  • Been ‘ordinarily resident’ in the UK for 3 years prior to the start of the studentship - (For non-EU citizens, this must NOT have been in full time education.)
    This means they must have been normally residing in the UK (apart from temporary or occasional absences). This does not apply to UK nationals. 

For more information, download this PDF.

How to apply

Applications for the PhD are processed through the Natural History Museum.

To apply, please send the following documents to the Postgraduate Office:

  • Curriculum vitae
  • Covering letter outlining your interest in the PhD position, relevant skills training, experience and qualifications for the research, and a statement of how this PhD project fits your career development plans
  • Names of two academic referees

The deadline for applications is 6 January 2020.

Any questions?

If you have any questions about the project please contact

Main supervisor: Dr Anne Jungblut


The Natural History Museum

Main supervisor: Dr Anne Jungblut

Imperial College London/NHM

Co-supervisor: Dr Andy Purvis


Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K (2017) Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS microbiology ecology, 1;93(5). 

Frąc M, Hannula SE, Bełka M, Jędryczka M (2018) Fungal Biodiversity and Their Role in Soil Health. Frontiers in Microbiology 9: 707

Hudson LT, Newbold T, Contu S, Hill SLL, Lysenko I, De Palma A et al. (2017) The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) Project. Ecology and Evolution 7: 145-188

McGill B 2015 Land use matters. Nature 520: 38-39.

Mahnert A, Moissl-Eichinger C, Berg G (2015) Microbiome interplay: plants alter microbial abundance and diversity within the built environment. Frontiers in Microbiology 6: 887

Wassermann B, Müller H, Berg G (2019) An Apple a Day: Which bacteria do we eat with organic and conventional apples? Frontiers in Microbiology 10: 1629

Science and Solutions for a Changing Planet (SSCP) doctoral training partnership

This is a joint project between The Science and Solutions for a Changing Planet (SSCP) Doctoral Training Partnership at Imperial College London and The Natural History Museum.

Funded by