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

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Beneficial microbiome(s) towards the future of sustainable agriculture

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

Agricultural research has long focused efforts into tapping into the potential of using the microbiome to limit fertilizer and pesticide use. This has boosted the search for beneficial microorganisms that associate with plants, providing them with increased nutrition among other benefits. Research on beneficial microbiomes has risen over the last few years and established itself as key towards sustainable agricultural practices.

The objective of this project is to address the mechanisms of microbe recruitment to the plant microbiome and screen soils for microbes with a beneficial effect on plant growth.

The microorganisms living around and within plant roots constitute their root microbiome. Many of these microorganisms are fungi and bacteria that contribute to the plants growth, by providing increased nutrition or resistance to pest and/or pathogen attacks. Thus, these are of extreme interest to plant production and to assure sustainable agricultural practices. However, it is not yet known how plants and microorganism establish these relationships and how the recruitment of these organisms takes place.  Furthermore, whether the plant is the main recruiter of the organisms surrounding it or whether these are recruited by the existing microbes in the soil is still not completely clear. We hypothesize that the microorganisms that influence plant growth are in turn recruited by the microorganisms already in the soil.


1.      Monitor plant fitness (health and nutritional status) in different soils.

2.      Analyze soil and root microbiota in different soils using classical and bioinformatics methods.

3.      Setup competition/synergy assays with the isolated microorganisms.

4.      Evaluate plant growth promoting phenotypes under different soil conditions and after inoculation with isolated microorganisms.

Work environments:
We expect you to be enthusiastic, dedicated and eager to learn. In return, we provide a stimulating, international research environment.


Methods used:Molecular biology, microbiology, amplicon sequencing with Illumina MiSeq, plant phenotyping, plant genotyping, bioinformatics, plant physiology, plant nutrition
Keywords:Sustainability, Microbiome, Plant, Green agriculture, Microbiology, Molecular biology
Project home page:
Supervisor(s): Prof Barbara Ann Halkier, Assistant Professor Deyang Xu