BBSRC NLD Doctoral Training Partnership: Core microbiomes in agro-ecosystems: Unravelling the effects of 125 years manure and fertilizer treatments in grassland soils using network ecology

   School of Natural and Environmental Sciences

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  Prof Darren Evans, Dr S Zytynska, Dr Alison Bennett  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

In an era of ecosystem degradation and climate change, maximizing microbial functions in agro-ecosystems has become a prerequisite for the future of global agriculture (Toju et al. 2018). However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Developing interdisciplinary research strategies to optimize microbiome functions in agroecosystems is a research priority. Recent advances in molecular biology and complexity science now allow for the rapid construction of ‘core microbiomes’, with informatics now providing an opportunity to identify their constituent members and characteristics (Guseva et al. 2022, Bennett et al. 2019). Moreover, advances in transcriptomics technology allows for novel examinations of cellular processes, but this remains largely unexplored in a community ecology context.

This project will develop an ecological network approach to examine how manure and fertiliser treatments affect the structure of and dynamics of soil microbe-plant interactions, and how this affects yield. Specifically, it will use the Palace Leas grazing and hay cutting experiment (established at Newcastle University’s Cockle Park farm in 1896)- the world’s longest-running grassland experiment. State-of-the art species-interaction networks will be created using DNA-metabarcoding and metagenomics. The project will address the following questions:

1) What is the structure of core soil microbiomes in grasslands and is this affected by fertilizer/manure treatment?

2) Do changes in plant-microbe ecological network structures affect plant transcriptomes, with a specific focus on yield?

3) Using the long-term data, what are the main biotic and abiotic drivers of changes in yield?

The project will be the first to link soil microbe-plant network structure with yield, significantly advancing our understanding of the biodiversity-ecosystem function relationship. By gaining a mechanistic understanding of the linkages between below-ground interactions and the transcriptome of target grass species (Festuca spp.), the project will ultimately identify which core microbiomes are associated with highest yield, allowing novel areas of development for sustainable agriculture. The student will benefit from rotations at both Newcastle University (Network Ecology Group) and Liverpool University (Plant Microbe interactions, transcriptomics), including possible research trips to partners at Ohio State University, where they will receive unique, state-of-the-art training in molecular biology, bioinformatics, network ecology and transcriptomics. As part of NU Farms, the student will have access to the Palace Leas research platform, on-farm laboratories and dedicated shuttle-bus between Cockle Park farm and campus.


Applications should be made by emailing [Email Address Removed] with:

  • a CV (including contact details of at least two academic (or other relevant) referees);
  • a covering letter – clearly stating your first-choice project, and optionally 2nd ranked project, as well as including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project(s) and at the selected University;
  • copies of your relevant undergraduate degree transcripts and certificates;
  • a copy of your IELTS or TOEFL English language certificate (where required);
  • a copy of your passport (photo page).

A GUIDE TO THE FORMAT REQUIRED FOR THE APPLICATION DOCUMENTS IS AVAILABLE AT Applications not meeting these criteria may be rejected.

In addition to the above items, please email a completed copy of the Additional Details Form (as a Word document) to [Email Address Removed]. A blank copy of this form can be found at:

Informal enquiries may be made to [Email Address Removed] 

The deadline for all applications is 12noon on Monday 15th January 2024.


Part-Time Study Options

All NLD DTP PhDs are available as part time or full time, with part time being a minimum of 50% of full time. Please discuss potential part time arrangements with the primary supervisor before applying to the programme.

Project CASE Status

This project is not a CASE project. While individual applicant quality is our overriding criterion for selection, the NLD DTP has a commitment to fund 8 CASE projects per year - as such, CASE projects may be favoured in shortlisting applicants when candidates are otherwise deemed to be equal or a consensus on student quality cannot be reached. 

Agriculture (1) Biological Sciences (4) Computer Science (8) Environmental Sciences (13)

Funding Notes

BBSRC NLD DTP programme – starting October 2024.
UKRI provide the following funding for 4 years:
• Stipend (2023/24 UKRI rate £18,622)
• Tuition Fees at UK fee rate (2023/24 rate £4,712)
• Research support and training grant (RTSG)
Note - UKRI funding only covers UK (Home) fees. The DTP partners have various schemes which allow international students to join the DTP but only be required to pay home fees. Home fees are already covered in the UKRI funding, meaning that successful international candidates do not need to find any additional funding for fees.


1) Network science: Applications for sustainable agroecosystems and food security. (2022) Perspectives in Ecology and Conservation 20 (2), 79-90.
2) Potentials and pitfalls in the analysis of bipartite networks to understand plant–microbe interactions in changing environments. (2019) Functional Ecology 33 (1), 107-117.
3) Impaired microbial N-acyl homoserine lactone signalling increases plant resistance to aphids across variable abiotic and biotic environments. (2022) Plant Cell Environ, 45, 3052-3069.
4) Microbial-mediated plant growth promotion and pest suppression varies under climate change. (2020) Frontiers in Plant Science, 11, 1385.
5) Soil microbial diversity impacts plant microbiota more than herbivory. (2021) Phytobiomes. 5(4): 408-417.
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