IAP-25-029

When nutrients turn toxic: how metals shape microbial coexistence

Every living ecosystem on Earth, from the human gut to the open ocean, is a community of species living side by side. Knowing how and why these ecosystems form, survive, change, or collapse, is key to spotting problems early and making smarter decisions to protect the health of the planet.

Bacterial communities are central to this story. They help humans and animals digest food, keep plants and soils healthy, and break down waste in rivers and oceans. Like all living things, bacteria need nutrients, including metals such as iron, zinc, and copper. These metals help bacteria make energy, build cellular parts, and defend against stress. But there is a twist – at high doses, these same metals become toxic, damaging the very same cellular machineries that they support.

To explain which species can and cannot live together, and why, ecologists have developed a powerful mathematical framework known as “coexistence theory”. However, this theory assumes nutrients are purely good and toxins purely bad, overlooking cases where a single substance, like a metal, is good in small doses but bad in large doses. This “toxic nutrient” pattern is not unique to metals. Many life-sustaining resources like water, oxygen, nitrogen, and phosphorus, can also turn harmful at high doses. This leaves a blind spot in our ability to explain and predict how Earth ecosystems respond to changing environments.

In this project, you will test the exciting hypothesis that toxic nutrients fundamentally shape which species can live together in bacterial ecosystems and beyond.

Depending on your background and interests, you will focus on experimental microbial ecology, theoretical ecology (mathematical modelling), or a combination of both. Whatever your chosen methodological focus, you will first study how the population of each bacterial species responds to metal supply. This will help you predict how a community of bacteria behaves. To test your predictions, you will create synthetic communities containing two or more species. You will track how the population of each species and the whole community to metal supply. You will answer questions such as: If we know the basic growth properties of each species, can we predict which species can or cannot live together in a community with a given amount of metal? How does the community change if metal supply changes? What happens if a new species invades or a critical species dies? Crucially, why?

In the laboratory, you will need to carry out bacterial cultures and co-cultures under high-throughput and highly controlled conditions. You will vary the metal supply in these cultures, engineer mutant strains of bacteria that differ in how they take up metals, track bacterial growth, and measure cellular metal content and metal-dependent gene expression. Where interesting bacteria-bacteria interactions are observed (for example via secretion of metal-binding metabolites), you will identify these metabolites using multi-omics approaches.

In mathematics, you will build on existing consumer-resource mathematical frameworks to include the behaviour of metals as toxic nutrients, carry out mathematical analyses in MatLab and other softwares, and create interactive, on-line apps (such as VisualPDE.com) that visually display your mathematical models and allow other researchers to also explore toxic nutrients.

Year 1

– Familiarise yourself with literature on metals in biology, microbial ecology, and coexistence theory.
– Gain proficiency in laboratory experiments and/or mathematical modelling.
– Begin work with single-species cultures.

Year 2

– Continue work with single-species cultures.
– Begin work with multi-species communities.
– Present your progress at a local conference or symposium.

Year 3

– Complete work with single-species cultures.
– Continue work with multi-species communities, including studies of interspecific interactions via metal cross-feeding or metal competition.
– Prepare thesis outline.

Year 3.5

– Complete work with multi-species communities.
– Present your progress at a major or international conference.
– Write thesis and prepare for viva.
– Prepare work for publication and app development.

Scientific training:

To succeed in this project, you will need to have a strong foundation in any one of the following subjects: microbiology, natural sciences, mathematics, or ecology. You will build on this foundation and learn how to conduct collaborative, inter-disciplinary research involving microbiology, ecology, and mathematics. Regardless of your chosen project focus (whether experimental and/or theoretical), you will learn fundamental concepts in microbiology and microbial ecology, and in theoretical ecology. Experimentally, you will gain skills in genetics, molecular biology, bacterial culture and co-culture, as well as high-throughput omics data and analyses. Theoretically, you will gain skills in mathematical modelling, as well as adapting and applying mathematical techniques in dynamical systems, statistics, and coexistence theory. In any case, you will build your confidence in formulating a scientific research question and in choosing/designing the most appropriate approaches to answer that question.

You will also acquire transferable skills, including time management, experimental planning, hypothesis generation, data interpretation, and statistical analyses. You will develop your communication skills by participating and contributing to weekly meetings with Supervisor 1’s group and additional regular meetings with the broader project team. These will expose you to different ways of working and help you build collaborative skills.

Opportunities for career development:

Current and past students in the group have contributed to co-supervising undergraduates, teaching in undergraduate practicals, outreach, and leadership activities. Like all our students, you will have opportunities to present at conferences and to co-author publications.
You will also build networking skills by attending and presenting at conferences.

Research environment:

At Durham Biosciences, you will join Dr Karrera Djoko’s group, a vibrant, friendly, supportive group all working in metals in microbiology (3 PhD students, 1 postgraduate Master’s, 2 undergraduates). You will also become part of the larger, interactive Metals@Durham (3 groups) and the Ecology, Evolution, and Environment (12 groups) research groupings in the department. The Djoko group already collaborates with Dr Denis Patterson’s and Dr Andrew Krause’s groups in Durham Mathematical Sciences. Through them, you will join the highly active Applied Mathematics Section (10 faculty, 7 postdocs, 5 PhD students) in Mathematical Sciences, which holds weekly lunches and seminars. You will also conduct a placement at Dr Katherine Duncan’s laboratory at Newcastle University Biosciences Institute, and interact with an interdisciplinary group focused on microbial metabolomics (1 RA, 2 PhD students, 3 undergraduates).