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A new way of thinking about biofilm formation

Primary Supervisor: Dr Tim Overton, School of Chemical Engineering

Secondary supervisor: Dr Francisco Fernandez-Trillo

PhD project title: A new way of thinking about biofilm formation

University of Registration: University of Birmingham

Project outline:

Biofilms are a major mode of microbial life on earth, and impact our lives due to their profound effects in clinical and industrial settings. Bacteria often form biofilms as a response to stressful environmental conditions, and biofilms are frequently more resistant to biological, chemical, and physical stresses (eg antibiotics; acids and other chemicals; and fluid flow / cleaning;) than planktonic bacteria. Understanding biofilm formation is key to improving health (chronic wounds, nosocomial and medical device-related infections), industrial safety (eliminating contamination of foods and other products, preventing fouling that can cause industrial accidents) and lowering emissions (biofilms on ships massively increase fuel use).

Biofilms have been defined by Donlan and Costerton (2002) as “a microbially derived sessile community characterized by cells that are irreversibly attached to a substratum or interface or to each other, are embedded in a matrix of extracellular polymeric substances that they have produced, and exhibit an altered phenotype with respect to growth rate and gene transcription”. The traditional model (Fig. 1) describes biofilm formation on a solid surface, comprising five stages: initial (reversible) attachment; irreversible attachment; proliferation and microcolony formation; maturation; and dispersion.

Figure 1. Traditional model of biofilm formation. The matrix is shown in green.

However, there is growing evidence that the traditional 5-step model for biofilm formation might be an oversimplification, and new models have been proposed. A summary of models for biofilm formation is shown in Fig. 2.

Figure 2. A newer model for different modes of biofilm formation.

The traditional model for biofilm formation is shown at the bottom, and is not discounted. However, it may also be noted that cell aggregates form in the liquid medium, which can settle to the bottom; could these settled aggregates form a biofilm? Are aggregates a biofilm, in that they make their own matrix? In addition, pellicle formation is encompassed by this new model. Pellicles are ‘floating’ biofilms that form at the air-liquid interface and are the major mode of biofilm formation in some species such as Bacillus subtilis; E. coli can also form pellicles under certain growth conditions. Pellicle formation has been postulated by a number of models, including extension from the wall of a growth vessel, and formation by floating ‘rafts’ of bacteria.

The Overton lab’s previous work with biofilms has focused on use of E. coli biofilms as platforms for biocatalysis (Tsoligkas et al., 2011). This led on to work investigating the fundamentals of E. coli biofilm formation (Leech et al., 2020) and discovery of pellicles formed by E. coli K-12 strains under certain growth conditions. We have worked in collaboration with the Fernandez-Trillo lab on use of polymers for directing bacterial physiology and behaviour, including formation of clusters and biofilms.

In this project we will put together ideas around formation of biofilms, pellicles and aggregates of cells, and investigate how each structure differs. Do aggregates and pellicles have similar structural properties to biofilms attached to surfaces? What environmental signals trigger the switch from single-celled planktonic growth to biofilm, aggregate or pellicle formation? Under what circumstances can cells change from an aggregate to a biofilm or a pellicle, and what are the regulatory and structural changes that occur under these circumstances? The project will be guided by current research and focus on E. coli initially, although may diversify to other organisms such as Pseudomonas aeruginosa. Polymers will be used as a key tool for directing bacterial behaviour. We will use flow cytometry and microscopy techniques, as well as standard molecular microbiology approaches (eg mutants, reporter genes) and some physical science analytical methods (eg hydrophobicity, surface charge of bacteria).

References

  1. Donlan RM, Costerton JW. (2002) Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev. doi: 10.1128/cmr.15.2.167-193.2002.
  2. Tsoligkas AN, Winn M, Bowen J, Overton TW, Simmons MJ, Goss RJ. (2011) Engineering biofilms for biocatalysis. Chembiochem. doi: 10.1002/cbic.201100200.
  3. Leech J, Golub S, Allan W, Simmons MJH, Overton TW. (2020) Non-pathogenic Escherichia coli biofilms: effects of growth conditions and surface properties on structure and curli gene expression. Arch Microbiol. doi: 10.1007/s00203-020-01864-5.

BBSRC Strategic Research Priority: Renewable Resources and Clean Growth: Industrial Biotechnology. Understanding the Rules of Life: Microbiology

Techniques that will be undertaken during the project:

  • Standard microbiological methods – culture in liquid media and biofilm formats
  • Molecular microbiology methods – use of mutants, cloning, reporter gene assays
  • Physical analytical methods - goiniometry, surface energy determination
  • Microscopy – Fluorescence and confocal microscopy to study biofilm, aggregate and pellicle structure and composition

Contact: Dr Tim Overton, University of Birmingham