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Microbial establishment on growing rhizoplanes

Principal Supervisor: Dr. Miriam Gifford, School of Life Sciences

Co-supervisor: Lionel Dupuy, The James Hutton Institute; Nicola Holden, The James Hutton Institute

PhD project title: Microbial establishment on growing rhizoplanes

University of Registration: University of Warwick

Project outline:

Scientific background: Microbial activity in soil and associations with plants are essential to nutrient availability, soil biodiversity and fertility. Plants are active in the colonization process and secrete compounds that stimulate or repress specific soil microbes [1]. Bacteria use various strategies to exploit carbon compounds released from plant roots, including surface attachment, motility or biofilm formation [2]. The rhizoplane is the physical site where microbes attach to the surface of plant cells and thus the location of microbe-plant exchange of critical chemical signals that encourage or block interactions. This rhizoplane interaction is essential for plants to overcome microbial pathogens but also foster mutualistic microbe associations [3].

Objectives: This project will provide a first detailed and quantitative analysis of the mechanisms of early microbial establishment of the rhizoplane. This project will focus on growing root tips, where exudation is high and where root surfaces are mostly free of microbes. The project will build on material and recent technological advances from our labs, inc. plant and microbial genetic material, Fluorescence-Activated Cell Sorting (FACS), transparent soil and imaging systems, and models developed recently.

Outcomes: The project will provide data on largely unknown processes: how fast microbes attach on the rhizoplane, what are the mechanisms that allow early colonization of the root, and what types of plant-microbe communications are involved.

Program of work: The student will initially develop a model system to study the basic mechanisms underlying colonization of the rhizoplane. This will include:

[M0-M7] The identification of bacterial species with contrasting colonization patterns and model plant species suitable to quantitative live imaging of bacterial density along the root. A collection of microbe/plant lines and species with traits or mutations affecting their ability to form a colonized rhizoplane, e.g. microbial mutants affected in their mobility and ability to attach, or plants with variations in their exudation profile or ability to sense and respond to elicitors.

[M7-M12] A FACS system to segregate attached and non-attach microbes/plant cells. FACS experiments will be used for both genetic analyses of cell responses to microbial attachment and to parameterize a model for surface attachment. Work could focus initially on border cells that can be extracted without enzymatic digestion of the cell wall.

[M12-M15] Develop a microcosm system for quantitative imaging of microbial colonization in gels and transparent soil.

[M15-M20] The project will then explore how mobility (of both root and microbial cells), adhesion and root-microbe communications influence the colonization of the root tip. Simple experiments will be run to calibrate a model of microbial colonization of the root tip [7]. The model will be calibrated for a reference microcosm system. Parameters such as root elongation rate, size of elongation zone, microbial growth rate, attachment rate, chemotactic parameter will be required to make predictions of microbial densities along the root.

[M20-M36] In the final stage of the project, experiments will combine a range of soil conditions, molecular genetic tools, live imaging and model simulations to analyses how modifications of key components of the mobility, adhesion and communication systems affect the colonization of the root tip.


  • Dennis et al (2010) FEMS Microbiol Ecol 72:313-327.
  • Rossez et al (2014) Environ Microbiol 16: 2181-2195.
  • Berendsen et al (2012) Trends Plant Sci 17: 478-486.
  • Schwessinger and Ronald (2012) Annu Rev Plant Biol 63: 451-482.
  • Gourion et al (2015) Trends Plant Sci 20: 186-194.
  • Weston et al (2012) Mol Plant Microbe Interact 25: 765-778.
  • Dupuy & Silk 2015 Vadose Zone J revision.

 BBSRC Strategic Research Priority: Food Security

Techniques that will be undertaken during the project:

The student will develop skills and expertise in 5 principal subject-specific areas:

  • The student will develop skills in microbiology and plant biology (supervision training).
  • Supervision will be given training in microscopy and live imaging biological systems.
  • The student will develop extensive skills in image analysis (supervision training).
  • The student will learn the principles of mathematical modelling (supervision training).
  • The student will also acquire generic skills in statistics and quantitative analysis of experimental data (in house supervision and BIOSS training).

The student will also receive training in generic research skills:

  • The student will be taught the writing of scientific articles and how to communicate the results of research to the plant science / soil science community.
  • The student will develop oral presentation skills by giving talks and presenting posters to conferences, e.g. SEB meetings, GARNet or UKPlant Sci (UKPSF) UK-based meetings. The student will participate in group meetings and interact with other members of the department by presenting progress in the form of internal seminars (Institute seminars and at University of Warwick seminars).
  • The student will learn how to communicate to non-scientific audiences and develop skills in outreach and realising impact by participating in the development of institute web pages and contributing to open days.
  • Finally, the successful candidate will interact with scientists from various backgrounds (plant biologists, microbiologists, soil scientists and modellers), and will develop research skills for collaborative work in a strongly multidisciplinary environment - scientific skills of outstanding relevance for early career researchers.

Contact: Miriam Gifford, School of Life Sciences