Know your enemy: a mathematical framework for competition in bacterial communities

Bacteria are found in almost every facet of the natural and manmade worlds. Nearly all bacteria live in biofilms. Biofilms are social communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion and plant protection, chronic infections and industrial biofouling. They are hallmarked by the production of an extracellular polymeric matrix. Bacterial biocontrol agents are designed to assist the growth of crops by increasing nutrient availability and uptake and preventing infection by pathogenic strains of microbes. The naturally occurring soil-borne bacterium Bacillus subtilis is commonly utilised in this context. It is now widely accepted that a better understanding of naturally occurring biocontrol and growth promoting agents will help drive sustainable agriculture in the future. This will enable food production to keep pace with the exploding human population whilst reducing the use of environmentally damaging manmade pesticides and fertilizers

In order to be successful as a biocontrol agent B. subtilis has to successfully compete with the resident species. Naturally, within the soil environment this will include other non-kin (i.e. genetically different) B. subtilis strains. Therefore as a first and essential step, our aim is to uncover the diverse ways Bacillus subtilis achieves dominance in the presence of non-kin isolates. 

To establish the hierarchy of dominance between the different isolates, we have already established mixed pairwise co-culture biofilms in the lab. The outcome of the interaction between the pairs of strains was intriguing. In this project we will use mathematical modelling to better understand the underlying mechanisms and to set and rapidly test hypotheses identifying any patterns in the hierarchy. The mathematical models will be able to characterise both the “well-mixed” and spatially extended situations. In the former, ODE-based models will be employed for population dynamics of mixed cultures testing hypotheses regarding:

o            Relative inoculum densities

o            Timing and form of signalling (e.g. diffusive or cell-to-cell)

o            Use (abuse) of common goods

o            Costs associated with competing/dominating/cooperating

o            Tools of war (e.g. contact mediated vs diffusible toxins)

Spatially extended models will be based on Individual Based Models (IBM) or Partial Differential Equations (PDE) depending on which level of colony maturity is under investigation. (Young colonies can more appropriately be modelled as a collective of individual cells, whereas mature biofilms and heterogeneous distributions of biomass and thus are amenable to modelling via PDE). 

 For informal enquiries about the project, contact Professor Fordyce Davidson (f.a.davidson@dundee.ac.uk)

For general enquiries about the University of Dundee, contact doctoralacademy@dundee.ac.uk

Our research community thrives on the diversity of students and staff which helps to make the University of Dundee a UK university of choice for postgraduate research. We welcome applications from all talented individuals and are committed to widening access to those who have the ability and potential to benefit from higher education.

QUALIFICATIONS

Applicants must have obtained, or expect to obtain, a UK honours degree at 2.1 or above (or equivalent for non-UK qualifications), and/or a Masters degree in a relevant discipline. For international qualifications, please see equivalent entry requirements here: www.dundee.ac.uk/study/international/country/.

English language requirement: IELTS (Academic) overall score must be at least 6.5 (with not less than 6.0 in writing and not less than 5.5 in reading, listening and speaking). The University of Dundee accepts a variety of equivalent qualifications; please see full details of the University’s English language requirements here: www.dundee.ac.uk/guides/english-language-requirements.

APPLICATION PROCESS

Step 1: Email Professor Fordyce Davidson (f.a.davidson@dundee.ac.uk) to (1) send a copy of your CV and (2) discuss your potential application and any practicalities (e.g. suitable start date).

Step 2: After discussion with Professor Davidson, formal applications can be made via our direct application system. When applying, please follow the instructions below:

 Apply for the Doctor of Philosophy (PhD) degree in Mathematics on our direct application system.

 Mathematics : Study : University of Dundee

This project is suitable for the three-year route or the four-year route as agreed with the lead supervisor. Please select the study mode (full-time/part-time) and start date agreed with the lead supervisor.

In the Research Proposal section, please:

-       Enter the lead supervisor’s name in the ‘proposed supervisor’ box

-       Enter the project title listed at the top of this page in the ‘proposed project title’ box

In the ‘personal statement’ section, please outline your suitability for the project selected.