Synthetic Ecosystems

What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can synthetic organisms be used to change endangered ecological communities and rescue them from collapse? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? These and other questions define a rapidly emerging research programme at the interface between synthetic biology, ecology and quantitative modelling.

The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. As we move toward advanced technological engineering of cells and organisms, the possibility of bioengineering ecosystems — from the gut microbiome to wildlands — opens several fundamental questions that will require quantitative models to find answers. In our lab, we explore these problems across three nested scales of complexity. At the smallest scale, test-tube ecosystems hosting a relatively low number of interacting species allow us to study the basic principles of synthetic ecological interactions: mutualism, competition, parasitism and their engineered variants. At the mesoscale, closed ecosystems or ecospheres provide model systems for understanding how confined communities maintain diversity and function over long periods — a problem with direct relevance to space exploration and life support systems. At the macroscale, we study how engineered organisms might be deployed within existing ecosystems to modify their trajectories and prevent catastrophic shifts.

A common thread across these scales involves using mathematical models that help us understand the implications of nonlinear interactions and predict potential outcomes. This systems biology view connects with the traditional quantitative study of ecological assemblies through population dynamics but extends it through the incorporation of designed genetic circuits and engineered metabolic interactions. We study ecological hypercycles — cooperative networks of microbial species where each member produces a resource needed by another — as a foundation for building self-sustaining synthetic communities. These designs draw inspiration from natural mutualistic networks but incorporate synthetic safeguards against evolutionary escape and collapse.

We also explore the role of viruses in synthetic ecosystem dynamics. Despite their tiny contribution to biomass, viruses are acknowledged as crucial players in the dynamics of microbiomes, yet they remain understudied within the synthetic biology framework. The impact of engineered phages and their potential role as vectors for ecosystem engineering is an open frontier that we are approaching through mathematical models that introduce the virome in an explicit manner.

The potential outcomes of synthetic ecosystem designs and their limits are relevant to multiple disciplines, including biomedical engineering — where engineered microbiomes could restore dysbiotic communities — astrobiology, where the creation of self-sustaining ecosystems in closed environments is essential for planetary exploration, and Earth system science, where large-scale bioengineering of landscapes represents a new and potentially transformative tool for confronting the ecological consequences of global warming.