The Soil Microbiome in Legume Rotations

Grain legumes (pulses) are an important arable break crop in the UK, fixing nitrogen through Rhizobia to benefit following crops, and providing a vital source of protein in food and feed. Demand for “home-grown” vegetable protein in the human diet is increasing, yet legume cropping frequency is constrained by the build-up of soil-borne pathogens with persistent resting spore stages. While several of these pathogens are known, the dynamics of increase and decline are not well understood, as is the behaviour of antagonistic, beneficial organisms. Additionally, some pathogenic organisms may not yet have been identified, due to inability to culture them, or through symptomless infection. New sequencing technologies offer great potential to understand the soil microbiome and rhizosphere community.

The PhD project will apply metagenomics analyses to explore potential differences in the microbiome in soils that have been deliberately intensively cropped with legumes, compared with those where no legumes have been cultivated in order to improve understanding of species composition and dynamics, and how potential differences are influencing nodulation. Metagenomics data will be obtained using next-generation sequencing targeting multiple barcoding genes to identify known species and operational taxonomic units (OTUs) to begin to characterise potential differences between the contrasting rotations.

The project is focused towards enhancing fundamental understanding of the legume crop-microbiome interactions and elucidating which microorganisms and associated factors can positive or negatively influence crop productivity. The work will extend microbiome profiling to soils obtained from pea and field bean crops with contrasting cultivation histories and different rotational practices to investigate effects on species diversity, particularly where foot-rot disease has been observed. Insight gained from wider scale profiling of field sites over successive cropping seasons will be used to begin develop legume soil health bio-indicators and metagenomics data will be utilised to construct phylogenies to compare species profiles associated with healthy and less productive land.

The candidate will also investigate microbiome dynamics over the growing season, testing for changes in species diversity and abundance, comparing pea and bean cultivated in both virgin and previously cropped soils. The student will investigate modelling approaches exploiting sequence and environmental data to test whether it is possible to predict how different host genotypes may influence soil microbial populations across rotations.

Finally, in an effort to elucidate potential genetic variation in the ability to nodulate with rhizobia, form mycorrhizal associations, and influence the range or quantity of beneficial and deleterious microflora, a panel of pea and faba beans will be screened to identify novel sources of variation to contribute to enhance pulse crop performance and provide new sources of linked markers for plant breeders. The project relates to NIAB’s faba bean research programme and the PhD project will extend to investigating the interaction of soil microbiome components and plant genotype.

About NIAB

Historically the National Institute of Agricultural Botany, NIAB’s central research objective is to bridge the gap between the fundamental understanding of plant biology and our ability to apply that knowledge in practice. NIAB is affiliated with the University of Cambridge, and works closely with researchers in a number of areas, including the new joint Crop Science Centre. For individuals desiring not only to learn but to make an impact, this is a vibrant and exciting place to conduct a PhD.

See details of the University's Entry Requirements here. 

All applications need to be submitted through the University’s Applicant Portal. Note there is an application fee.