Project at Aberystwyth University: Awakening the dormant soil microbiome

Healthy and productive soils are foundational for agriculture. In turn, the microbial communities of soil are critical determinants and indicators of soil health. But life is tough for soil microbes, so many soil microbes lie dormant, awaiting better times. A teaspoon of soil can contain a billion microbes, but up to 80% of them are asleep. This project explores the topic of dormancy and activation within soil microbes to understand the rules of life, death, and in-between, within soil. In essence, for healthy and productive agri-ecosystems, is it better to let sleeping bugs lie?

This project offers an exciting opportunity at the frontiers of bioscience. We are starting to appreciate the exceptional biodiversity and importance of soil microbes, but few appreciate that most are asleep. Understanding the factors governing the balance between dormancy and activity within soil microbes has the potential to transform our understanding of soil microbiology, and ultimately unlock the full potential of the soil microbiome. While different paradigms of dormancy have been explored in laboratory cultures for decades, few studies have ventured into the real world. This PhD will take this ambitious but logical next step forward.

This PhD project will use an experimental system developed at Aberystwyth University for modulating dormancy in microbes, and apply it to the agricultural context by evaluating microbial dormancy and its interactions with soil health and plant productivity, as well as the role of dormancy in the environmental persistence in the important animal pathogen, Mycobacterium bovis.

You will learn how to express and purify recombinant proteins, apply them as treatments in robustly-designed experiments, and techniques for microbiome and metagenome analyses. Your development as a researcher will be supported by a multidisciplinary team of experienced microbiologists at Aberystwyth University (Dr Arwyn Edwards, Dr Amanda Gibson, and Professor Luis Mur). A component of the project will be hosted by bioinformatics experts at Queen’s University Belfast led by Dr Rachel Wheatley. Successful completion of the PhD will provide you with skills in microbiology, genomics and bioinformatics, plant growth and pathogen handling.

Training opportunities: You will gain training through the project in microbiological experimental design and execution, microbiome and metagenome analyses using DNA and RNA, protein expression and characterization and metagenomic bioinformatics. You also have specific training opportunities for CL2 work, environmental genomics, and media outreach.

Project supervision style: As a minimum you will attend monthly individual formal meetings with the AU supervisors, with Wheatley joining as required, however the Edwards group holds a weekly lab meeting for presentation of work to celebrate progress and help overcome barriers. In common with AU practice, Edwards and Mur both have “open door” policies which welcomes frequent informal interaction as required. You will be welcome to contact any supervisor at any point. Feedback on drafts (e.g. literature review, manuscripts, presentations) will be provided as agreed between you and supervisor, and the writing up process is closely supported throughout. Standard practice within the group is to hold a project initiation meeting with all supervisors and expectations and responsibilities confirmed for all concerned as regards working patterns, leave, meetings, feedback, authorship, data management, group citizenship and other operational factors.

Student profile: Candidates with an academic background in molecular microbiology and/or microbial ecology are sought for this PhD.

How to Apply: Applications will be by an online application form only. Do not send CVs. Please go to the FoodBioSystems website to see guidance to applicants, information on academic and funding eligibility and language proficiency.

Equality Diversity and Inclusion: The FoodBioSystems DTP is committed to equality, diversity and inclusion. Our actions to promote diversity and inclusion are detailed on the  FoodBioSystems DTP website and include: Offering reasonable adjustments at interview for shortlisted candidates who have disclosed a disability or specific learning difference; Guaranteed interview and applicant mentoring schemes for applicants, with UK home fees status, from eligible under-represented ethnic groups. These are opt-in processes.