University of Dundee

EASTBIO: A synthetic community approach to decipher the genetic basis of plant-microbiota interactions in the rhizosphere

This project aims to enhance sustainable crop production by resolving the genetic basis of the interactions between plants and microbiota inhabiting the rhizosphere, the interface between plant roots and soil. The rhizosphere microbiota has the potential of positively impacting the plant’s growth, development, and health representing renewable alternative to agrochemicals. The plant genome is a determinant of the rhizosphere microbiota, providing a foundation for the development of innovative crops better adapted to low-input agriculture. However, the complexity of interactions occurring in soil makes it difficult to resolve the genetic basis of microbiota recruitment in the rhizosphere. An attractive avenue to deconvolute this complexity is to expose plants to a microbiota of known taxonomic composition under controlled conditions, so called Synthetic Communities (SynComs). The use of SynComs permits us to mimic microbiota properties, discern their impact on plant growth and development, and analyse the effect of multiple plant genotypes on microbial recruitment.  

In this project the student will use a bacterial collection we recently developed for the global crop Barley (Hordeum vulgare) to pursue three interconnected objectives. First, using both cultivation-dependent and -independent assays the student will capitalise on the collection to assemble and determine the colonisation reproducibility of SynComs of different taxonomic composition. The most stable SynComs will be then investigated for their growth promotion potential on a set of reference barley genotypes. As the available bacterial collection is sequenced, the student will attempt to identify features of the bacterial genomes putatively required for growth promotion.  In the third objective of the project, the student will use the most promising SynCom to determine the genetic variation for bacterial responsiveness in wild and domesticated barley genotypes. Using existing barley genomic resources, the student will then attempt at identifying host determinants of SynCom colonisationThese lines of investigation will provide novel insights into the genetic basis of plant-microbiota interactions in the rhizosphere and set the stage for innovative approaches to sustainably enhance crop production. 


On completion of their PhD, the student will have gained new skills encompassing microbiology, plant genetics, rhizosphere biology, sequencing data analysis and multivariate statistics. The student will be based in the Division of Plant Sciences and will interact with the newly established International Barley Hub (IBH The student will profit from the interactions with a diverse and multidisciplinary scientific community, including other eastBIO PhD students, and will use state-of-the-art facilities.  


Further reading: 


  1. Mahdi L,  Miyauchi S,  Uhlmann C, Garrido-Oter R,  Langen GWawra LNiu Y, Robertson-Albertyn S, Bulgarelli D, Parker J,  Zuccaro A. (2021)The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. press in The ISME Journal. 

  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.