University of Dundee

EASTBIO: Harnessing host-microbiota interaction to sustainably enhance plant’s micronutrients uptake

Supervisors: Dr Davide Bulgarelli, Division of Plant Sciences and Dr Timothy George (The James Hutton Institute) 

This project aims at enhancing the plant’s uptake of mineral micronutrients by identifying the genetic determinants underpinning plant-microbiota interactions in the rhizosphere, the interface between roots and soil.  

The uptake of mineral micronutrients (such as Fe, Zn, Cu, Mn) is essential for plant growth, development and health.  In turn, this process defines the nutritional value of crop products and therefore impacts animal and human health accordingly. The rhizosphere microbiota has the potential to positively contributing to this process and decouple profitably yield from the application of synthetic fertilisers. However, microbiota applications are currently hampered by the lack of genetic insights into the establishment of plant-microbe interactions in the rhizosphere. For instance, we need to know how plant genetic variation shapes the colonisation of beneficial members of the microbiota. In addition, we need to understand the role individual microorganisms have in promoting plant’s micronutrient uptake. Finally, we need to know whether targeted modification of the plant genome will allow us to predictably manipulate host-microbiota interactions for sustainable mineral uptake. 

In this project, the student will embark a two-pronged approach capitalising on existing plant genetic resources and the establishment of a Synthetic Community (SynCom) approach to identify plant and microbial genes underpinning of host-microbiota interactions in the rhizosphere. The staple crop Barley (Hordeum vulgare L) will be used as an experimental model and the initial focus will be on locally adapted varieties, previously characterised for their superior performance under micronutrient-limiting conditions and for which useful cross populations which are genomically characterised exist.   

In particular, the student will discern the contribution of plant genetic variation on microbiota colonisation by performing genetic mapping investigations using metagenomic information as an “external” quantitative trait.  In parallel, the student will identify, and isolate individual members of the rhizosphere microbiota putatively implicated in micronutrient mobilisationAkin to the “Koch’s postulates for the microbiota”, the student will then use the identified microbes in a SynCom approach to infer causal relationships between microbial colonisation and plant’s micronutrient uptake.  Finally, by using speed-breeding and other innovative approaches in genetics (e.g., genome editing), the student will attempt to manipulate the plant genome to expedite the recruitment of beneficial members of the microbiota in the rhizosphere.  

At the completion of this project, the student will have strengthened new and existing skills in a range of disciplines, including metagenomics, plant genetics, plant physiology and rhizosphere biology. Of notethis project will be developed at the newly established International Barley Hub (IBH  International – Barley Hub), where the student will profit from the interactions with a diverse and multidisciplinary scientific community, including other eastBIO PhD students, and state-of-the-art facilities. This environment will expedite the translation of the basic science gathered in this project into translational applications for the agro-biotech sector, for example genetic markers for breeding selection as well as microbial inoculants aimed at sustainably enhancing plat’s micronutrient uptake, both locally and globally.  

Further reading: 


  1. Alegria Terrazas R, Balbirnie-Cumming K, Morris JA, Hedley PE, Russell J, Paterson E, Baggs EM, Fridman E, Bulgarelli D. 2020. A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota. Scientific Reports. 10(1):Article 12916. 
  1. Escudero-Martinez C, Bulgarelli D. (2019). Tracing the evolutionary routes of plant-microbiota interactions. Current Opinion in Microbiology. 49:34-40  
  1. Schmidt SB, George TS, Brown LK, Booth A, Wishart J, Hedley PE, Martin P, Russell J, Husted S. (2019) Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to manganese limitation. Annals of botany 123:831-843.