We work primarily with bacteria isolated from natural environments. There are millions of bacteria in every pinch of soil, so there is an enormous choice in selecting species to work with. A typical day would involve collecting samples from the ‘wild’ and returning them to the lab. Since bacteria are so abundant, the samples are then diluted in sterile water. The diluted samples are transferred onto agar plates, where individual cells proliferate into visible colonies. Colonies can then be picked into separate vials. Most bacteria collected in this way can be stored for years at -80C and remain viable. Using this technique we have created a living archive of hundreds of different bacterial strains, which we then use in experiments to understand their ecology.
Our research also encompasses predators and pathogens of bacteria. Just like for all of us, bacteria can be infected by viruses (‘phage’). Phage are a major cause of bacterial mortality in many environments, so we are interested in their role in bacterial community dynamics. Some lytic phage can be visualised directly because they burst bacterial cells as they proliferate. These can be visualised on agar plates as clearings on lawns of bacteria. We have begun hunting for phage in our different study systems, and hope this will be a component of our future research. We also study the main predators of the bacterial world: protists. Protists are single-celled organisms that hunt bacteria. Well-known examples include amoeba, which engulfs its prey, but there are many other feeding modes. Using bacteria, phage, and protists, we can begin to assemble fully-functional food webs that have complex dynamics and that begin to resemble natural ecosystems.
The video shows a small protist in the group Cercozoa foraging for bacteria.