Microorganisms such as bacteria often form colonies on surfaces. Examples of such colonies are various “biofilms” found in sewage pipes, on teeth, rotten food etc., but also much less complex structures that biologists grow in Petri dishes filled with agar and a suitable nutrient broth. Even such single-species colonies incubated in a controlled environment exhibit many interesting features: they can grow into many different shapes (regular, wrinkled, fractal etc.), they can disperse over time or come together to create larger clusters, and show many forms of social interactions (cooperation, competition, they can even play rock-paper-scissor).
I am interested in how mechanical interactions between bacterial cells in a microcolony (a small colony of a few hundred micrometres across) determine the shape and the speed of growth of the colony, and also fixation probabilities of new mutants that spontaneously arise during growth. I have been working on this with several different people: Oskar Hallatschek, Pietro Cicuta, Davide Marenduzzo, Rosalind Allen, Wilson Poon, Fred Farrell, and my PhD students Kuba Pastuszak, and Joshua Williams.
Apart from scientific value, research on microbial colonies generates some pretty images and videos. Some of them can be found below.
Computer simulation of rod-shaped, elastic bacteria growing in a narrow, vertical tube. The camera follows the moving front of the colony. Different colours correspond to different progenies of the few initial bacteria. Mechanical repulsion between the bacteria leads to cells separating into “sectors”.
A small fragment of a simulated colony of E. coli. Colours correspond to different layers of bacteria. Green = the most bottom layer. With F. Farrell, see this publication.
Diarmuid Lloyd has made this image showing a collision between two bacterial colonies. The collision leads to a very interesting zig-zag pattern similar to what can be observed when two fluids mix. The green cells have a conjugative plasmid which can be passed to the black cells and is seen as the red area at the interface of the two colonies.
Left: A microcolony of E. coli. Cells form “domains” in which all cells are aligned in approximately the same direction (different colours). Image by Diarmuid Lloyd. Middle: a simulated colony. As in the experimental image cells have been colour-coded according to their orientations (blue=vertical, red=horizontal). Right: “cosmic background radiation map” – a simulated, much bigger colony.
Left: a 3d colony of bacteria growing inside the agarose gel. The colony has a “lenticular” shape and we (Wilson, Diarmuid and I) would like to understand what causes the colony to grow into this particular shape. Middle: “Bacterial galaxy” – another 3d reconstruction. Little “stars” in the background are colloidal particles used to track the movement of the agarose around the colony. Image by D. Lloyd. Left: bright-field image of 3d colonies obtained by my former Master student Michal Tomaszewski.
My PhD student Joshua Williams is now trying to explain these results by simulating how microbial colonies interact with agarose gel. The image below shows a simulated colony trapped between the glass (below the colony) and the agarose (above the colony). The first layer of agarose has been made visible in the right-hand image.
My former PhD student Kuba Pastuszak and I wrote a paper on horizontal transfer of genetic information between cells in bacterial colonies. We investigated the process of bacterial conjugation, in which junction is created between two cells (donor and acceptor) and a copy of a small DNA molecule called the plasmid is transferred from the donor to the acceptor. The image shows transconjugants (blue) emerging at the interface of a colony of donor (red) and a colony of acceptor (green) cells, and a pattern of sectors emerging during growth of a mixed colony of donors and acceptors. We show in the paper that mechanical interactions between donor and acceptor cells caused by the presence of the junction stabilize the “mating pair” and increase the rate of conjugation.