Project details – Institut for Plante- og Miljøvidenskab - Københavns Universitet

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Identification of phytochemical cues to assemble beneficial root microbiota

Main area:
Target group:Biology-Biotechnology, Agriculture, Environmental Science, Natural Resources
Educational level:Master, Project outside course scope, Bachelor
Project description:

Plants health depends on dynamic interactions with associated bacteria and fungi. Deciphering the driving force that shapes the microbiome has great potential for sustainable crop production. The goal of this project is to advance our understanding of the factors that shapes the root microbiota.

Background: Similar to the microbial communities in the human gut, plants accommodate a specific root microbiota to mitigate biotic and abiotic stresses. Most land plants live in symbiosis with arbuscular mycorrhizal fungi as means to ensure nutrient uptake, but plants in the Brassicales order have apparently no mycorrhiza. However, beneficial endophytes transfer phosphor to its non-mycorrhizal host Arabidopsis thaliana under low phosphor conditions. Massive transcriptomic and metabolomic changes upon phosphor starvation show very strong upregulation of glucosinolate biosynthetic genes and their products. We hypothesize that Brassicales-specific glucosinolates in root exudate are important for attracting beneficial endophytes.


a)     Monitor plant fitness under phosphor starvation conditions of wildtype, glucosinolates biosynthetic null mutants and transporter mutants

b)     Analyze root-associated microorganisms in wildtype and mutants grown -/+ P

c)     Metabolite profiling of root exudates and microbiome of wildtype and mutants

d)     Evaluate associations between root exudates and microbiota in different genotypes for assemblage of beneficial root microbiota

Methodologies: molecular biology, heterologous expression in yeast and plant hosts, amplicons sequencing with Illumina MiSeq, LC-MS analytical chemistry, transport engineering, plant genotyping, bioinformatics on candidate gene family.

Keywords: root microbiome, transport biology, yeast, plant, metabolomics

Work environments: We expect you to be enthusiastic, dedicated and eager to learn and advance your skills in many disciplines (e.g. research, oral and written presentations). In return, we provide a stimulating, international research environment.  

Main supervisor Prof. Barbara Ann Halkier, DynaMo Center of Excellence, PLEN, Frederiksberg. Email:

Co-supervisor: Dr.Deyang Xu, Email:  



Methods used:Molecular biology;Metabolite profiling;genome sequencing;bioinformatics;
Keywords:root microbiom, transport biology, yeast, plant, metabolomics
Supervisor(s): Barbara Ann Halkier;Deyang Xu