PhD project: Deciphering species coexistence using microbial microcosms

Project description

How does Nature sustain such a diverse variety of biological species? This question has long preoccupied scientists, including Darwin. Not surprisingly, there exist a variety of theories to explain species coexistence, but it is very difficult to test them experimentally in realistic ecosystems. Microbes - microscopic living organisms that exist in huge numbers almost everywhere in the environment, and in our bodies - provide a potentially very exciting test case for understanding species coexistence, since we can easily grow them in the lab and manipulate and sample them in many replicates. In our lab, we have been studying a beautiful model system for studying microbial species coexistence. This consists of Winogradsky columns: plastic tubes filled with pond sediment and water, which are sealed and exposed to light. Over a few months, these develop coloured layers corresponding to different types of bacteria, and they cycle nutrients (carbon and sulphur) in a self-sustained way that can maintain species diversity over periods of years. We have found out many interesting things about the role of stochasticity versus determinism, system size, response to environmental perturbations, etc, in these microcosms, but up to now we have not looked carefully at the mechanisms underlying the astonishing species diversity that we see in these systems. In this project, we will investigate species diversity in Winogradsky column microcosms, using one of several of the following approaches:

1. We will try to make "synthetic" Winogradsky columns out of known bacterial species. This would allow us to really control which of the various postulated mechanisms of species coexistence are operating in our microcosms.

2. We will carry out detailed data analyses of our large collection of previous experimental datasets, to test whether the correlations between species abundances within a single microcosm give clues to what might be driving species coexistence.

3. We will build simple theoretical models of the population dynamics that could be happening in our microcosms, to try to see what models best fit our data. 

Which of these approaches we focus on depends on the student's preference and expertise, but the project will involve a significant fraction of experimental work.  Prior biological knowledge or microbiology experience is not required.

Project supervisors

  • (School of Physics & Astronomy, University of Edinburgh)
  • Dr Andrew Free (School of Biological Sciences, University of Edinburgh)

The project supervisors welcome informal enquiries about this project.

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