Job description

Job summary

The Ransome Lab at the Silwood Park Campus of Imperial College London is seeking a microbial/ computational ecologist with strong quantitative skills interested in developing analytical pipelines to understand the role of the microbiome in supressing the pathogens of one of the world’s most important staple crops, wheat (T. aestivum). We aim to do this through the analysis of multi-omic data from field surveys and manipulations of the extant soil microbiome. The project has two overarching goals: 1) to develop a lab-to-field pipeline for microbiome optimization in arable soils, focusing specifically on suppression of the take-all fungus, Gaeumannomyces tritci, in the wheat rhizosphere; and 2) to advance our fundamental understanding of microbial community dynamics in complex environments. This project, a collaboration between the Waring, Pawar, Graystock and Bell labs, aims to find a new approach to supress this disease, which causes between 5-50% loss of production globally of one of the world’s most important staple crops.

Through field surveys of soil associated bacterial, fungal and viral communities and microbial directed artificial selection in the lab, we will develop soil microbiomes that exhibit suppression of take-all disease in the greenhouse setting. Your role will be to develop bioinformatic pipelines, data analysis techniques, and innovative models to better understand the role of the soil microbiome in supressing G.tritci using metabarcoding and metagenomic data from the field and the lab. You will help to identify microbial taxa and/or metabolic networks which most strongly influence crop performance. You will work closely with other PDRAs on bacterial and fungal data and will lead the charge to understand the role of viruses in these communities. This may lead to companion experiments in the lab or greenhouse which you will help to design, allowing us to better understand the role of viruses in supressing crop pathogens. This will help you to advance your own career interests, with opportunities to develop collaborations that extend beyond our core group. Additionally, you will have the opportunity to connect with stakeholders who are collaborating directly with our project (including CABI, Rothamsted Research) and the wider collaborative network of the Ransome Lab.

Duties and responsibilities

Your primary task will be to develop bioinformatic and analytical pipelines to explore how interactions among fungi, bacteria and viruses in the wheat rhizosphere promote (or suppress) wheat growth and resistance to G. tritici. You will focus on exploring viral communities in metagenomic data with the opportunity to develop experiments to further explore these communities in the laboratory. You will also have a leadership role in coordinating and managing all sequencing data for this project.

You will be assisted in this effort by a team of four PDRAs, technicians and post-graduate students, who will be engaged in the laboratory optimisation of the disease-suppressing inoculum, molecular and culture-based studies of microbial physiology, and using Genome-Scale modelling and ecological theory to understand and predict the dynamics of microbial communities. By working closely together, this team has the potential to significantly advance our capacity to manage complex microbiomes to improve the sustainability of agriculture. You will therefore be expected to interact with your colleagues in the laboratory, in the field, and through regular group meetings to discuss analytical approaches. You will also have the opportunity to supervise undergraduate and post-graduate student projects. Finally, you will be provided the resources to advance your own career, through mentorship, and professional development opportunities. 

You will be expected to communicate the findings of your research through conference presentations and scientific publications. Additionally, you will have the opportunity to connect directly with farmers and other local stakeholders who are collaborating with our research group.

Essential requirements

Essential criteria:

• Hold a PhD (or equivalent) in microbial ecology, computational ecology, or related field or a closely related discipline

• Excellent scientific communication skills, as evidenced by presentations at scientific conferences and publications in peer-reviewed journals
• Evidence of effective collaborative work in a team environment
• Demonstrated research experience in microbial ecology
• Experience with the management/organisation of large datasets
• Strong quantitative skills with experience of scientific programming in Python or R

Desirable criteria:

• Experience processing omics data in a reproducible, open and transparent way
• Experience using high-performance computing
• Experience with either process-based or numeric simulation modelling
• Experience working in a microbial laboratory
• Experience working on experiments with complex designs
• A valid driver’s licence (for traveling to/from field sites)

Further information

*Candidates who have not yet been officially awarded their PhD will be appointed as Research Assistant within the salary range £40,694 - £43,888 per annum.

Please note this position is available full time, fixed term for 3 years.

Applicants should provide a CV and a cover letter (two pages maximum) explaining their qualifications for the role.

Long-listed candidates will be contacted to complete a Belbin Profile (a free login will be provided) and a short ‘challenge question’ directly relevant to the role. Please note this is a team activity that will help with outlining development opportunities it won’t be a decision making tool.

We anticipate holding interviews for these candidates in late November.

Should you require any further details on the role please contact Emma Ransome at e.ransome@imperial.ac.uk with ‘Green Microbiome PDRA’ in the subject line

The College is currently trialling a Work Location Framework. Hybrid working may be considered for this role and the role holder may be expected to work 60% or more of their time onsite, with 40% the minimum time spent onsite. The opportunity for hybrid working will be discussed at interview.

The College is a proud signatory to the San-Francisco Declaration on Research Assessment (DORA), which means that in hiring and promotion decisions, we evaluate applicants on the quality of their work, not the journal impact factor where it is published. For more information, see https://www.imperial.ac.uk/research-and-innovation/about-imperial-research/research-evaluation/

The College believes that the use of animals in research is vital to improve human and animal health and welfare. Animals may only be used in research programmes where their use is shown to be necessary for developing new treatments and making medical advances. Imperial is committed to ensuring that, in cases where this research is deemed essential, all animals in the College’s care are treated with full respect, and that all staff involved with this work show due consideration at every level.

http://www.imperial.ac.uk/research-and-innovation/about-imperial-research/research-integrity/animal-research/

We are committed to equality of opportunity, to eliminating discrimination and to creating an inclusive working environment for all. We therefore encourage candidates to apply irrespective of age, disability, marriage or civil partnership status, pregnancy or maternity, race, religion and belief, gender reassignment, sex, or sexual orientation. We are an Athena SWAN Silver Award winner, a Disability Confident Leader and a Stonewall Diversity Champion.

Documents

• Job Description.pdf