Distribution of Functions in Microbiomes

Microbes live in complex communities where they interact in various ways with other microbes. One type of interactions is the exchange of metabolic intermediates among microbes with different metabolic capabilities. This results in a distributed, collective metabolism. The organising principles, structure and features of these distributed metabolic networks are not well understood. We explore:

• What factors that determine the degree of metabolic distribution in microbial ecosystems (Alyssa)
• The effects of functional redundancy and bacterial interaction networks on functional stability in microbial communities (Anna)
• How nutrient utilisation strategies affect microbial coexistence (Megan)

Physiological models for communities and in non-steady-state environments

Marine microbes play a massive role in the global carbon cycle by breaking down organic matter. However, predicting how these complex communities will respond to climate change, such as rising temperatures and ocean acidification, remains a major challenge. While we have a good grasp of how individual species react to these stressors, we know much less about what happens in diverse communities where populations and interactions constantly shift. By observing how communities interact, compete, and adapt under changing conditions, we are developing new predictive models to understand the future of the marine carbon cycle.

• Predicting marine microbial community response to rising temperatures and acidification through proteome allocation. (Nittay)
• How distributed metabolism in microbial communities can be modelled mathematically, taking into account temporally and spatially heterogeneous conditions. (Benjamin)

Predictive phage ecology across scales

Viruses are everywhere life exists, including within the bacterial communities that support life across Earth in soils, oceans, and ourselves. The viruses that infect bacteria – known as phages – are so abundant that they often outnumber their bacterial hosts. Phages transform the membership and activities of bacterial communities, which in turn impacts the health of ecosystems around the globe. Therefore, it is essential that we understand how they are being affected by the climate crisis – both to predict how our world is changing and to harness the power of microbiomes to create a more sustainable future.

We are currently far from being able to predict how interactions between phages and bacteria shape the ecosystem-level functions of microbial communities. Our research addresses several questions about phages across scales of ecological complexity: Do trade-offs in phage traits define ecological strategies? How do bacterial physiology and environmental factors tune phage-host interactions? And which phage and host traits are predictive of their dynamics? For this research, we are using both model phages and natural phage-host populations from plant microbiomes, which harbor enormous, unexplored viral diversity and are key targets for sustainability-oriented microbiome engineering. (Rachel)