How do interaction mechanisms shape microbial ecosystems?

Details

Microbial ecosystems are some of the richest on the planet. For example, a single gram of soil can contain over a million different microbial species. This is an extraordinary amount of diversity for such a minute system, and how this diversity is maintained remains a mystery.

Theoretical ecologists explain diversity using models built with ‘interactions’, the impact of one species on the growth of another. Microbes generally interact indirectly through changes to their chemical environment. Fierce competition for limited nutrients can cause one species to drive another to extinction, while secretion of beneficial metabolic by-products can help other community members. Many of these indirect mechanisms between species can occur simultaneously, leading to complex composite interactions in which the shifting balance between mechanisms in different chemical environments can create different interaction outcomes. For example, the presence of a toxin may cause one species to help another, while its absence may cause a harmful outcome instead.

In this project, we will explore how the indirect basis of microbial interactions impacts their emergent ecology. Using a combination of ecological theory and controlled, lab-based experiments, we will address questions such as:

– How do antibiotics change microbial interactions?

– Is diversity maintained by mutual metabolic dependencies between microbes?

– Can we engineer communities by chemically controlling interactions?

The answers to these questions may have implications for human health (helping us to understand the role of microbes in the gut), planetary health (through microbes’ role in global carbon cycling) and agriculture (by helping us to suppress soil pathogens and boost nitrogen-fixing organisms).

As part of the project, you will have the opportunity to learn cutting-edge techniques using the University of Sheffield’s world-class research facilities, including microscopy, high-throughput genomics and metabolomics. You will also learn how to integrate mathematical ecosystem modelling with experimental data.

Our lab strongly supports cross-disciplinary approaches to research. We straddle the clusters of Molecular Microbiology and Ecology and Evolution, and you will have the opportunity to participate in the research culture of both through research seminars and social events. We are also integrated into a local network of researchers interested in applying ideas and techniques from physics to biological questions, which will provide the opportunity to develop partnerships with physicists and mathematicians outside the School of Biosciences.

Please apply for this project using this link: https://www.sheffield.ac.uk/postgraduate/phd/apply/applying

Funding Notes

Self-funded and externally funded students only

References

Key publication: https://doi.org/10.1111/ele.70027

Lab website: https://sites.google.com/sheffield.ac.uk/microbial-ecosystem-physics/home