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Unravelling the global microbiome of crop plants to improve sustainability and food security
Secondary Supervisor(s): Dr Ryan Mushinski, Dr Fabrizio Alberti, Chris Quince (Earlham Institute)
University of Registration: University of Warwick
BBSRC Strategic Research Priority:
Project Outline
Plants live in close association with complex communities of microbes which together constitute their ‘microbiome’. The microbiome interacts with the plant in numerous ways; some microbes are beneficial and promote plant growth, while others are pathogens which reduce crop yields. Understanding and harnessing interactions within the microbiome has enormous importance for devising net zero carbon emission sustainable agricultural systems while ensuring food and energy security, and also mitigating the threats posed by climate change and land degradation.
In collaboration with an international team of scientists (https://www.globalsustainableagriculture.org) you will use molecular approaches to investigate the factors which shape the microbiome of the world’s most important agricultural crops including wheat, maize and rice. You will focus on beneficial microbial groups which show promise to support the sustainable development of agricultural systems. Focussed experiments will then be conducted under controlled environment conditions to investigate the ways in which these microbes interact with plants and affect their growth and development.
You will use a range of methods including amplicon and metagenome sequencing, and quantitative PCR to profile the structure, abundance and functional characteristics of key microbial groups with specialized functional traits. There will also be scope to assemble and characterize microbial genomes using metagenomic sequences, and to isolate microbes and investigate plant-microbe interactions under controlled environment conditions. This could include studies of the spatial localization of microbes within root systems using advanced imaging techniques, and transcriptional and proteomic analysis of the interaction pathways.
References
Hilton, S., Picot, E., Schreiter, S., Bass, D., Norman, K., Oliver, A., Moore, J.D., Mauchline, T.H.,Mills, P.R., Teakle, G.R., Clark, I.M., Hirsch, P.R., van der Gast, D.J., Bending, G.D. (2021)Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale. Microbiome 9, 1-15.
Lidbury, I.D.E.A., Borsetto, C., Murphy, A.R.J., Botrtill, A., Jones, A.M.E., Bending, G.D. et al. (2021) Niche-adaptation in plant-associated Bacteroidetes favours specialization in organic phosphorus mineralization. ISME J 15, 1040-1050.
Picot, E., Hale, C.C., Hilton, S., Teakle, G.R., Schäfer, H., Huang, Y., Perryman, S., West, J.S., Bending, G.D. (2021) Contrasting responses of rhizosphere bacterial, fungal, protist and nematode communities to nitrogen fertilization and crop genotype in field grown oilseed rape (Brassica napus). Frontiers in Sustainable Food Systems 5, 88.
Albornoz, F.E., Orchard, S., Standish, R.J., Dickie, I.A., Bending, G.D. et al. (2021) Evidence for niche differentiation in the environmental responses of co-occurring mucormycotinian fine rootendophytes and glomeromycotinian arbuscular mycorrhizal fungi. Microbial Ecology 81, 864-873.
