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Exploring the ecological and evolutionary impacts of novel agricultural probiotics on naiive microbial communities

Project Description

Probiotic inoculants represent a major tool in the shift towards more sustainable agriculture. The clearest benefits are seen in legumes, like Soya, which forms associations with nitrogen-fixing bacteria - rhizobia - allowing them to obtain nitrogen from the atmosphere and so reduce the need for carbon-intensive fertilizers. Providing crops with effective rhizobia strains can have impressive impacts on yield, especially when crops are being grown outside of their native ranges where their natural rhizobial partners are absent. However, the introduction of high densities of novel bacteria into the soil is likely to have consequences for the local microbial community which are largely unexplored. Novel bacteria may have ecological effects, e.g. washing out of local diversity, or evolutionary effects, e.g. by introducing novel genes to resident bacteria through horizontal gene transfer.

We have the opportunity to study these dynamics at an exciting moment: The UK is on the cusp of the widespread introduction of novel bacteria into a naïve microbial community. At present Soya is emerging as a novel - and sustainable - crop but their natural rhizobial partners (Soya-associated Bradyrhizobium - SABs) are absent from UK soils.

Project description

In this project, we will use mesocosm experiments combined with cutting-edge sequencing approaches to investigate the ecological and evolutionary effect of SAB introduction on the local microbiome in UK soils. The student will engage with Soya growers across the UK to identify sampling sites, design and conduct greenhouse experiments and develop analytical methods.

The supervisory team brings together an interdisciplinary team formed of experts in rhizobia, soil microbial diversity, bacterial evolution and horizontal gene transfer. Also, we have the support of our case partner, PlantWorksUK, who specialises in agricultural microbial inoculants. The student will, therefore, be able to acquire a broad set of lab skills (greenhouse experiments, microbiology and molecular biology), analytical techniques (statistics, bioinformatics) and experience in liaising with industry, including the opportunity to undertake a 3-month industrial placement with PlantWorksUK. The project will be primarily based at the University of Sheffield - which is ranked top 5 in the UK for student experience - with opportunities for secondments to work at the James Hutton Institute in Dundee - a world-leading institution for crop science.

This project will suit a motivated student interested in using ecology and evolution to support agricultural innovation. The student should have either a 2:1 honours degree + Masters (or equivalent) or first class honours in a relevant subject. This could be Biology, Microbiology, Agricultural Sciences or similar. Experience with either practical microbiology, horticulture or bioinformatics is desirable but not required.

Funding Notes

Fully funded studentships cover: (i) a stipend at the UKRI rate (at least £14,777 per annum for 2019-2020), (ii) research costs, and (iii) tuition fees. Studentship(s) are available to UK and EU students who meet the UK residency requirements.
This PhD project is part of the NERC funded Doctoral Training Partnership “ACCE” (Adapting to the Challenges of a Changing Environment View Website. ACCE is a partnership between the Universities of Sheffield, Liverpool, York, CEH, and NHM.
Shortlisted applicants will be invited for an interview to take place at the University of Sheffield the w/c 11th February 2019.


Kontopoulou, C.-K., Liasis, E., Iannetta, P.P.M., Tampakaki, A., Savvas, D. (2017) Impact of rhizobial inoculation and reduced N supply on biomass production and biological N2-fixation in common bean (Phaseolus vulgaris L.) grown hydroponically. Journal of the Science of Food and Agriculture 97, 4353-4361

Dos Santos, Alves, Silva, Rhem, James & Gross (2017) Diverse genotypes of Bradyrhizobium nodulate herbaceous Chamaecrista (Moench) Fabaceae, Caesalpinioideae) species in Brazil. Systematic and Applied Microbiology, 40, 69-79.

Hall, Brockhurst & Harrison (2017) Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria, Phil. Trans. R. Soc. B, 372 (1735)

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